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A glossary of bioinformatics terms

Original article published on the website bioinfbook.org

A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z

This glossary is combined from five web-based glossaries: [1] the National Center for Biotechnology Information (entries marked NCBI), [2] the Oak Ridge National Laboratory (entries marked ORNL), [3] the talking glossary at the National Human Genome Research Institute, [4] the SMART database, and [5] the protein folds glossary from the Structural Classification of Proteins website (SCOP)(these entries are modified). Additional web-based glossaries are listed in a table at the end of this glossary.

The glossaries are on-line at: 
[1]  http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/glossary2.html
[2]  http://www.ornl.gov/TechResources/Human_Genome/glossary/
[3]  http://www.genome.gov/page.cfm?pageID=10002096
[4]  http://smart.embl-heidelberg.de/help/smart_glossary.shtml
[5]  http://scop.mrc-lmb.cam.ac.uk/scop/gloss.html


A  [top]

Additive genetic effects
When the combined effects of alleles at different loci are equal to the sum of their individual effects. (ORNL)

Adenine (A) 
A nitrogenous base, one member of the base pair AT (adenine-thymine). 
See also: base pair (ORNL)

A fixed procedure embodied in a computer program. (NCBI)

The process of lining up two or more sequences to achieve maximal levels of identity (and conservation, in the case of amino acid sequences) for the purpose of assessing the degree of similarity and the possibility of homology. (NCBI)

Representation of a prediction of the amino acids in tertiary structures of homologues that overlay in three dimensions. Alignments held by SMART are mostly based on published observations (see domain annotations for details), but are updated and edited manually. (SMART)

A class that has the number of secondary structures in the domain or common core described as 3-, 4-, 5-, 6- or multi- helical. (SCOP)

A class that includes two major fold groups: sandwiches and barrels. The sandwich folds are made of two beta-sheets which are usually twisted and pack so their strands are aligned. The barrel fold are made of single beta-sheet that twists and coils upon itself so, in most cases, the first strand in the beta sheet hydrogen bond to the last strand. The strand directions in the two opposite sides of a barrel fold are roughly orthogonal. Orthogonal packing of sheets is also seen in a few special cases of sandwich folds (SCOP)

Alternative form of a genetic locus; a single allele for each locus is inherited from each parent (e.g., at a locus for eye color the allele might result in blue or brown eyes). (ORNL)

One of the variant forms of a gene at a particular locus, or location, on a chromosome. Different alleles produce variation in inherited characteristics such as hair color or blood type. In an individual, one form of the allele (the dominant one) may be expressed more than another form (the recessive one). (NHGRI)

Variation in alleles among members of the same species. (ORNL)

Alternative splicing 
Different ways of combining a gene's exons to make variants of the complete protein (ORNL)

Amino acid 
Any of a class of 20 molecules that are combined to form proteins in living things. The sequence of amino acids in a protein and hence protein function are determined by the genetic code. (ORNL)

An increase in the number of copies of a specific DNA fragment; can be in vivo or in vitro. 
See also: cloning (ORNL)

Animal model 
See: model organisms (ORNL)

Adding pertinent information such as gene coded for, amino acid sequence, or other commentary to the database entry of raw sequence of DNA bases. 
See also: bioinformatics (ORNL)

Each generation of offspring has increased severity of a genetic disorder; e.g., a grandchild may have earlier onset and more severe symptoms than the parent, who had earlier onset than the grandparent. 
See also: additive genetic effectscomplex trait (ORNL)

Nucleic acid that has a sequence exactly opposite to an mRNA molecule made by the body; binds to the mRNA molecule to prevent a protein from being made. 
See also: transcription (ORNL)

Programmed cell death, the body's normal method of disposing of damaged, unwanted, or unneeded cells. 
See also: cell (ORNL)

Array (of hairpins) 
An assemble of alpha-helices that can not be described as a bundle or a folded leaf. (SCOP)

Arrayed library 
Individual primary recombinant clones (hosted in phage, cosmid, YAC, or other vector) that are placed in two-dimensional arrays in microtiter dishes. Each primary clone can be identified by the identity of the plate and the clone location (row and column) on that plate. Arrayed libraries of clones can be used for many applications, including screening for a specific gene or genomic region of interest. 
See also: librarygenomic librarygene chip technology (ORNL)

Putting sequenced fragments of DNA into their correct chromosomal positions. (ORNL)

A technique that uses X-ray film to visualize radioactively labeled molecules or fragments of molecules; used in analyzing length and number of DNA fragments after they are separated by gel electrophoresis. (ORNL)

Autosomal dominant 
A gene on one of the non-sex chromosomes that is always expressed, even if only one copy is present. The chance of passing the gene to offspring is 50% for each pregnancy. 
See also: autosomedominant, gene (ORNL)

A chromosome not involved in sex determination. The diploid human genome consists of a total of 46 chromosomes: 22 pairs of autosomes, and 1 pair of sex chromosomes (the X and Y chromosomes). 
See also: sex chromosome (ORNL)

B  [top]

A cross between an animal that is heterozygous for alleles obtained from two parental strains and a second animal from one of those parental strains. Also used to describe the breeding protocol of an outcross followed by a backcross. 
See also: model organisms (ORNL)

Bacterial artificial chromosome (BAC) 
A vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on naturally occurring F-factor plasmid found in the bacterium E. coli. 
See also: cloning vector (ORNL)

Bacterial artificial chromosome (BAC)
Large segments of DNA, 100,000 to 200,000 bases, from another species cloned into bacteria. Once the foreign DNA has been cloned into the host bacteria, many copies of it can be made. (NHGRI)

See: phage (ORNL)

Structures are usually closed by main-chain hydrogen bonds between the first and last strands of the beta sheet, in this case it is defined by the two integer numbers: the number of strand in the beta sheet, n, and a measure of the extent the extent to which the strands in the sheet are staggered the shear number, S. (SCOP)

One of the molecules that form DNA and RNA molecules. 
See also: nucleotidebase pairbase sequence (ORNL)

Base pair (bp) 
Two nitrogenous bases (adenine and thymine or guanine and cytosine) held together by weak bonds. Two strands of DNA are held together in the shape of a double helix by the bonds between base pairs. (ORNL)

Base sequence 
The order of nucleotide bases in a DNA molecule; determines structure of proteins encoded by that DNA. (ORNL)

Base sequence analysis 
A method, sometimes automated, for determining the base sequence. (ORNL)

Behavioral genetics 
The study of genes that may influence behavior. (ORNL)

Can be antiparallel (i.e. the strand direction in any two adjacent strands are antiparallel), parallel (all strands are parallel each other) and mixed (there is one strand at least that is parallel to one of its two neighbours and antiparallel to the other). (SCOP)

The merger of biotechnology and information technology with the goal of revealing new insights and principles in biology. (NCBI)

The science of managing and analyzing biological data using advanced computing techniques. Especially important in analyzing genomic research data. 
See also: informatics (ORNL)

The use of biological organisms such as plants or microbes to aid in removing hazardous substances from an area. (ORNL)

A set of biological techniques developed through basic research and now applied to research and product development. In particular, biotechnology refers to the use by industry of recombinant DNA, cell fusion, and new bioprocessing techniques. (ORNL)

Birth defect 
Any harmful trait, physical or biochemical, present at birth, whether a result of a genetic mutation or some other nongenetic factor. 
See also: congenital, genemutationsyndrome (ORNL)

Bit score 
The value S' is derived from the raw alignment score S in which the statistical properties of the scoring system used have been taken into account. Because bit scores have been normalized with respect to the scoring system, they can be used to compare alignment scores from different searches. (NCBI)

Bits scores
Alignment scores are reported by HMMer and BLAST as bits scores. The likelihood that the query sequence is a bona fide homologue of the database sequence is compared to the likelihood that the sequence was instead generated by a "random" model. Taking the logarithm (to base 2) of this likelihood ratio gives the bits score. (SMART)

Basic Local Alignment Search Tool. (Altschul et al.) A sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query. The initial search is done for a word of length "W" that scores at least "T" when compared to the query using a substitution matrix. Word hits are then extended in either direction in an attempt to generate an alignment with a score exceeding the threshold of "S". The "T" parameter dictates the speed and sensitivity of the search. For additional details, see one of the BLAST tutorials (Query or BLAST) or the narrative guide to BLAST. (NCBI)

A computer program that identifies homologous (similar) genes in different organisms, such as human, fruit fly, or nematode. (ORNL)

Blocks Substitution Matrix. A substitution matrix in which scores for each position are derived from observations of the frequencies of substitutions in blocks of local alignments in related proteins. Each matrix is tailored to a particular evolutionary distance. In the BLOSUM62 matrix, for example, the alignment from which scores were derived was created using sequences sharing no more than 62% identity. Sequences more identical than 62% are represented by a single sequence in the alignment so as to avoid over-weighting closely related family members. (Henikoff and Henikoff) (NCBI)

An array of alpha-helices each oriented roughly along the same (bundle) axis. It may have twist, left-handed if each helix makes a positive angle to the bundle axis, or, right-handed if each helix makes a negative angle to the bundle axis. (SCOP)

C  [top]

Diseases in which abnormal cells divide and grow unchecked. Cancer can spread from its original site to other parts of the body and can be fatal. 
See also: hereditary cancersporadic cancer (ORNL)

Candidate gene 
A gene located in a chromosome region suspected of being involved in a disease. 
See also: positional cloningprotein (ORNL)

Capillary array 
Gel-filled silica capillaries used to separate fragments for DNA sequencing. The small diameter of the capillaries permit the application of higher electric fields, providing high speed, high throughput separations that are significantly faster than traditional slab gels. (ORNL)

Something which causes cancer to occur by causing changes in a cell's DNA. 
See also: mutagen (ORNL)

An individual who possesses an unexpressed, recessive trait. (ORNL)

cDNA library 
A collection of DNA sequences that code for genes. The sequences are generated in the laboratory from mRNA sequences. 
See also: messenger RNA (ORNL)

The basic unit of any living organism that carries on the biochemical processes of life. 
See also: genomenucleus (ORNL)

Centimorgan (cM) 
A unit of measure of recombination frequency. One centimorgan is equal to a 1% chance that a marker at one genetic locus will be separated from a marker at a second locus due to crossing over in a single generation. In human beings, one centimorgan is equivalent, on average, to one million base pairs. 
See also: megabase (ORNL)

A specialized chromosome region to which spindle fibers attach during cell division. (ORNL)

Chimera (pl. chimaera) 
An organism that contains cells or tissues with a different genotype. These can be mutated cells of the host organism or cells from a different organism or species. (ORNL)

Chloroplast chromosome 
Circular DNA found in the photosynthesizing organelle (chloroplast) of plants instead of the cell nucleus where most genetic material is located. (ORNL)

Chromosomal deletion 
The loss of part of a chromosome's DNA. (ORNL)

Chromosomal inversion 
Chromosome segments that have been turned 180 degrees. The gene sequence for the segment is reversed with respect to the rest of the chromosome. (ORNL)

The self-replicating genetic structure of cells containing the cellular DNA that bears in its nucleotide sequence the linear array of genes. In prokaryotes, chromosomal DNA is circular, and the entire genome is carried on one chromosome. Eukaryotic genomes consist of a number of chromosomes whose DNA is associated with different kinds of proteins. (ORNL)

Chromosome painting 
Attachment of certain fluorescent dyes to targeted parts of the chromosome. Used as a diagnositic for particular diseases, e.g. types of leukemia. (ORNL)

Chromosome region p 
A designation for the short arm of a chromosome. (ORNL)

Chromosome region q 
A designation for the long arm of a chromosome. (ORNL)

An exact copy made of biological material such as a DNA segment (e.g., a gene or other region), a whole cell, or a complete organism. (ORNL)

Clone bank 
See: genomic library (ORNL)

Using specialized DNA technology to produce multiple, exact copies of a single gene or other segment of DNA to obtain enough material for further study. This process, used by researchers in the Human Genome Project, is referred to as cloning DNA. The resulting cloned (copied) collections of DNA molecules are called clone libraries. A second type of cloning exploits the natural process of cell division to make many copies of an entire cell. The genetic makeup of these cloned cells, called a cell line, is identical to the original cell. A third type of cloning produces complete, genetically identical animals such as the famous Scottish sheep, Dolly. 
See also: cloning vector (ORNL)

Cloning vector 
DNA molecule originating from a virus, a plasmid, or the cell of a higher organism into which another DNA fragment of appropriate size can be integrated without loss of the vector's capacity for self-replication; vectors introduce foreign DNA into host cells, where the DNA can be reproduced in large quantities. Examples are plasmids, cosmids, and yeast artificial chromosomes; vectors are often recombinant molecules containing DNA sequences from several sources. (ORNL)

Closed, Partly Opened and Opened 
For all-alpha structures describes the extent in which the hydrophobic core is screened by the comprising alpha-helices. Opened means that there is space for at least one more helix to be easily attached to the core (SCOP)

See: genetic code (ORNL)

Situation in which two different alleles for a genetic trait are both expressed. 
See also: autosomal dominantrecessive gene (ORNL)

See: genetic code (ORNL)

Coisogenic or congenic 
Nearly identical strains of an organism; they vary at only a single locus. (ORNL)

Comparative genomics 
The study of human genetics by comparisons with model organisms such as mice, the fruit fly, and the bacterium E. coli. (ORNL)

Complementary DNA (cDNA) 
DNA that is synthesized in the laboratory from a messenger RNA template. (ORNL)

Complementary sequence 
Nucleic acid base sequence that can form a double-stranded structure with another DNA fragment by following base-pairing rules (A pairs with T and C with G). The complementary sequence to GTAC for example, is CATG. (ORNL)

Complex trait 
Trait that has a genetic component that does not follow strict Mendelian inheritance. May involve the interaction of two or more genes or gene-environment interactions. 
See also: Mendelian inheritanceadditive genetic effects (ORNL)

Computational biology 
See: bioinformatics (ORNL)

In genetics, the expectation that genetic material and the information gained from testing that material will not be available without the donor's consent. (ORNL)

Any trait present at birth, whether the result of a genetic or nongenetic factor. 
See also: birth defect (ORNL)

Changes at a specific position of an amino acid or (less commonly, DNA) sequence that preserve the physico-chemical properties of the original residue. (NCBI)

Conserved sequence 
A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained essentially unchanged throughout evolution. (ORNL)

Group of cloned (copied) pieces of DNA representing overlapping regions of a particular chromosome. (ORNL)

Contig map 
A map depicting the relative order of a linked library of overlapping clones representing a complete chromosomal segment. (ORNL)

Artificially constructed cloning vector containing the cos gene of phage lambda. Cosmids can be packaged in lambda phage particles for infection into E. coli; this permits cloning of larger DNA fragments (up to 45kb) than can be introduced into bacterial hosts in plasmid vectors. (ORNL)

connection links secondary structures at the opposite ends of the structural core and goes across the surface of the domain. (SCOP)

Crossing over 
The breaking during meiosis of one maternal and one paternal chromosome, the exchange of corresponding sections of DNA, and the rejoining of the chromosomes. This process can result in an exchange of alleles between chromosomes. 
See also: recombination (ORNL)

The study of the physical appearance of chromosomes. 
See also: karyotype (ORNL)

Cytological band 
An area of the chromosome that stains differently from areas around it. 
See also: cytological map (ORNL)

Cytological map 
A type of chromosome map whereby genes are located on the basis of cytological findings obtained with the aid of chromosome mutations. (ORNL)

Cytoplasmic (uniparental) inheritance 
See: cytoplasmic trait (ORNL)

Cytoplasmic trait 
A genetic characteristic in which the genes are found outside the nucleus, in chloroplasts or mitochondria. Results in offspring inheriting genetic material from only one parent. (ORNL)

Cytosine (C) 
A nitrogenous base, one member of the base pair GC (guanine and cytosine) in DNA. 
See also: base pairnucleotide (ORNL)

D  [top]

Data warehouse 
A collection of databases, data tables, and mechanisms to access the data on a single subject. (ORNL)

A loss of part of the DNA from a chromosome; can lead to a disease or abnormality. 
See also: chromosomemutation (ORNL)

Deletion map 
A description of a specific chromosome that uses defined mutations --specific deleted areas in the genome-- as 'biochemical signposts,' or markers for specific areas. (ORNL)

See: nucleotide (ORNL)

A type of sugar that is one component of DNA (deoxyribonucleic acid). (ORNL)

A full set of genetic material consisting of paired chromosomes, one from each parental set. Most animal cells except the gametes have a diploid set of chromosomes. The diploid human genome has 46 chromosomes. 
See also: haploid (ORNL)

Directed evolution 
A laboratory process used on isolated molecules or microbes to cause mutations and identify subsequent adaptations to novel environments. (ORNL)

Directed mutagenesis 
Alteration of DNA at a specific site and its reinsertion into an organism to study any effects of the change. (ORNL)

Directed sequencing 
Successively sequencing DNA from adjacent stretches of chromosome. (ORNL)

Disease-associated genes 
Alleles carrying particular DNA sequences associated with the presence of disease. (ORNL)

DNA (deoxyribonucleic acid) 
The molecule that encodes genetic information. DNA is a double-stranded molecule held together by weak bonds between base pairs of nucleotides. The four nucleotides in DNA contain the bases adenine (A), guanine (G), cytosine (C), and thymine (T). In nature, base pairs form only between A and T and between G and C; thus the base sequence of each single strand can be deduced from that of its partner. (ORNL)

DNA bank 
A service that stores DNA extracted from blood samples or other human tissue. (ORNL)

DNA probe 
See: probe (ORNL)

DNA repair genes 
Genes encoding proteins that correct errors in DNA sequencing. (ORNL)

DNA replication 
The use of existing DNA as a template for the synthesis of new DNA strands. In humans and other eukaryotes, replication occurs in the cell nucleus. (ORNL)

DNA sequence 
The relative order of base pairs, whether in a DNA fragment, gene, chromosome, or an entire genome. 
See also: base sequence analysis (ORNL)

A discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function. (NCBI)

A discrete portion of a protein with its own function. The combination of domains in a single protein determines its overall function. (ORNL)

Conserved structural entities with distinctive secondary structure content and an hydrophobic core. In small disulphide-rich and Zn2+-binding or Ca2+- binding domains the hydrophobic core may be provided by cystines and metal ions, respectively.
Homologous domains with common functions usually show sequence similarities. (SMART)

Domain composition
Proteins with the same domain composition have at least one copy of each of domains of the query. (SMART)

Domain organisation
Proteins having all the domains as the query in the same order (Additional domains are allowed)). (SMART)

An allele that is almost always expressed, even if only one copy is present. 
See also: genegenome (ORNL)

Double helix 
The twisted-ladder shape that two linear strands of DNA assume when complementary nucleotides on opposing strands bond together. (ORNL)

Draft sequence 
The sequence generated by the HGP as of June 2000 that, while incomplete, offers a virtual road map to an estimated 95% of all human genes. Draft sequence data are mostly in the form of 10,000 base pair-sized fragments whose approximate chromosomal locations are known. 
See also: sequencingfinished DNA sequenceworking draft DNA sequence (ORNL)

A program for filtering low complexity regions from nucleic acid sequences. (NCBI)

E  [top]

E value 
Expectation value. The number of different alignents with scores equivalent to or better than S that are expected to occur in a database search by chance. The lower the E value, the more significant the score. (NCBI)
This represents the number of sequences with a score greater-than, or equal to, X, expected absolutely by chance. The E-value connects the score ("X") of an alignment between a user-supplied sequence and a database sequence, generated by any algorithm, with how many alignments with similar or greater scores that would be expected from a search of a random sequence database of equivalent size. Since version 2.0 E-values are calculated using Hidden Markov Models, leading to more accurate estimates than before. (SMART)

A method of separating large molecules (such as DNA fragments or proteins) from a mixture of similar molecules. An electric current is passed through a medium containing the mixture, and each kind of molecule travels through the medium at a different rate, depending on its electrical charge and size. Agarose and acrylamide gels are the media commonly used for electrophoresis of proteins and nucleic acids. (ORNL)

A process using high-voltage current to make cell membranes permeable to allow the introduction of new DNA; commonly used in recombinant DNA technology. 
See also: transfection (ORNL)

Embryonic stem (ES) cells 
An embryonic cell that can replicate indefinitely, transform into other types of cells, and serve as a continuous source of new cells. (ORNL)

See: restriction enzyme (ORNL)

A protein that acts as a catalyst, speeding the rate at which a biochemical reaction proceeds but not altering the direction or nature of the reaction. (ORNL)

One gene interfers with or prevents the expression of another gene located at a different locus. (ORNL)

Escherichia coli 
Common bacterium that has been studied intensively by geneticists because of its small genome size, normal lack of pathogenicity, and ease of growth in the laboratory. (ORNL)

The study of improving a species by artificial selection; usually refers to the selective breeding of humans. (ORNL)

Cell or organism with membrane-bound, structurally discrete nucleus and other well-developed subcellular compartments. Eukaryotes include all organisms except viruses, bacteria, and bluegreen algae. 
See also: prokaryotechromosome. (ORNL)

Evolutionarily conserved 
See: conserved sequence (ORNL)

Exogenous DNA 
DNA originating outside an organism that has been introducted into the organism. (ORNL)

The protein-coding DNA sequence of a gene. 
See also: intron (ORNL)

An enzyme that cleaves nucleotides sequentially from free ends of a linear nucleic acid substrate. (ORNL)

Expressed gene 
See: gene expression (ORNL)

Expressed sequence tag (EST) 
A short strand of DNA that is a part of a cDNA molecule and can act as identifier of a gene. Used in locating and mapping genes. 
See also: cDNAsequence tagged site (ORNL)

F  [top]

The first widely used algorithm for database similarity searching. The program looks for optimal local alignments by scanning the sequence for small matches called "words". Initially, the scores of segments in which there are multiple word hits are calculated ("init1"). Later the scores of several segments may be summed to generate an "initn" score. An optimized alignment that includes gaps is shown in the output as "opt". The sensitivity and speed of the search are inversely related and controlled by the "k-tup" variable which specifies the size of a "word". (Pearson and Lipman) (NCBI)

Filial generation (F1, F2) 
Each generation of offspring in a breeding program, designated F1, F2, etc. (ORNL)

Also known as Masking. The process of hiding regions of (nucleic acid or amino acid) sequence having characteristics that frequently lead to spurious high scores. See SEG and DUST. (NCBI)

In genetics, the identification of multiple specific alleles on a person's DNA to produce a unique identifier for that person. 
See also: forensics (ORNL)

Finished DNA Sequence
High-quality, low error, gap-free DNA sequence of the human genome. Achieving this ultimate 2003 HGP goal requires additional sequencing to close gaps, reduce ambiguities, and allow for only a single error every 10,000 bases, the agreed-upon standard for HGP finished sequence. 
See also: sequencingdraft sequence (ORNL)

Flow cytometry 
Analysis of biological material by detection of the light-absorbing or fluorescing properties of cells or subcellular fractions (i.e., chromosomes) passing in a narrow stream through a laser beam. An absorbance or fluorescence profile of the sample is produced. Automated sorting devices, used to fractionate samples, sort successive droplets of the analyzed stream into different fractions depending on the fluorescence emitted by each droplet. (ORNL)

Flow karyotyping 
Use of flow cytometry to analyze and separate chromosomes according to their DNA content. (ORNL)

Fluorescence in situ hybridization (FISH) 
A physical mapping approach that uses fluorescein tags to detect hybridization of probes with metaphase chromosomes and with the less-condensed somatic interphase chromatin. (ORNL)

Folded leaf 
A layer of alpha-helices wrapped around a single hydrophobic core but not with the simple geometry of a bundle. (SCOP)

The use of DNA for identification. Some examples of DNA use are to establish paternity in child support cases; establish the presence of a suspect at a crime scene, and identify accident victims. (ORNL)

Fraternal twin 
Siblings born at the same time as the result of fertilization of two ova by two sperm. They share the same genetic relationship to each other as any other siblings. 
See also: identical twin(ORNL)

Full gene sequence 
The complete order of bases in a gene. This order determines which protein a gene will produce. (ORNL)

Functional genomics 
The study of genes, their resulting proteins, and the role played by the proteins the body's biochemical processes. (ORNL)

G  [top]

Mature male or female reproductive cell (sperm or ovum) with a haploid set of chromosomes (23 for humans). (ORNL)

A space introduced into an alignment to compensate for insertions and deletions in one sequence relative to another. To prevent the accumulation of too many gaps in an alignment, introduction of a gap causes the deduction of a fixed amount (the gap score) from the alignment score. Extension of the gap to encompass additional nucleotides or amino acid is also penalized in the scoring of an alignment. (NCBI)

A position in an alignment that represents a deletion within one sequence relative to another. Gap penalties are requirements for alignment algorithms in order to reduce excessively-gapped regions. Gaps in alignments represent insertions that usually occur in protruding loops or beta-bulges within protein structures. (SMART)

GC-rich area 
Many DNA sequences carry long stretches of repeated G and C which often indicate a gene-rich region. (ORNL)

Gel electrophoresis 
See: electrophoresis (ORNL)

The fundamental physical and functional unit of heredity. A gene is an ordered sequence of nucleotides located in a particular position on a particular chromosome that encodes a specific functional product (i.e., a protein or RNA molecule). 
See also: gene expression (ORNL)

Gene amplification 
Repeated copying of a piece of DNA; a characteristic of tumor cells. 
See also: geneoncogene (ORNL)

Gene chip technology 
Development of cDNA microarrays from a large number of genes. Used to monitor and measure changes in gene expression for each gene represented on the chip. (ORNL)

Gene expression 
The process by which a gene's coded information is converted into the structures present and operating in the cell. Expressed genes include those that are transcribed into mRNA and then translated into protein and those that are transcribed into RNA but not translated into protein (e.g., transfer and ribosomal RNAs). (ORNL)

Gene family 
Group of closely related genes that make similar products. (ORNL)

Gene library 
See: genomic library (ORNL)

Gene mapping 
Determination of the relative positions of genes on a DNA molecule (chromosome or plasmid) and of the distance, in linkage units or physical units, between them. (ORNL)

Gene pool 
All the variations of genes in a species. 
See also: allelegenepolymorphism (ORNL)

Gene prediction 
Predictions of possible genes made by a computer program based on how well a stretch of DNA sequence matches known gene sequences (ORNL)

Gene product 
The biochemical material, either RNA or protein, resulting from expression of a gene. The amount of gene product is used to measure how active a gene is; abnormal amounts can be correlated with disease-causing alleles. (ORNL)

Gene testing 
See: genetic testinggenetic screening (ORNL)

Gene therapy 
An experimental procedure aimed at replacing, manipulating, or supplementing nonfunctional or misfunctioning genes with healthy genes. 
See also: geneinheritsomatic cell gene therapygerm line gene therapy (ORNL)

Gene transfer 
Incorporation of new DNA into and organism's cells, usually by a vector such as a modified virus. Used in gene therapy. 
See also: mutationgene therapyvector (ORNL)

Genetic code 
The sequence of nucleotides, coded in triplets (codons) along the mRNA, that determines the sequence of amino acids in protein synthesis. A gene's DNA sequence can be used to predict the mRNA sequence, and the genetic code can in turn be used to predict the amino acid sequence. (ORNL)

Genetic counseling 
Provides patients and their families with education and information about genetic-related conditions and helps them make informed decisions. (ORNL)

Genetic discrimination 
Prejudice against those who have or are likely to develop an inherited disorder. (ORNL)

Genetic engineering 
Altering the genetic material of cells or organisms to enable them to make new substances or perform new functions. (ORNL)

Genetic engineering technology 
See: recombinant DNA technology (ORNL)

Genetic illness 
Sickness, physical disability, or other disorder resulting from the inheritance of one or more deleterious alleles. (ORNL)

Genetic informatics 
See: bioinformatics (ORNL)

Genetic map 
See: linkage map (ORNL)

Genetic marker 
A gene or other identifiable portion of DNA whose inheritance can be followed. 
See also: chromosomeDNAgeneinherit (ORNL)

Genetic material 
See: genome (ORNL)

Genetic mosaic 
An organism in which different cells contain different genetic sequence. This can be the result of a mutation during development or fusion of embryos at an early developmental stage. (ORNL)

Genetic polymorphism 
Difference in DNA sequence among individuals, groups, or populations (e.g., genes for blue eyes versus brown eyes). (ORNL)

Genetic predisposition 
Susceptibility to a genetic disease. May or may not result in actual development of the disease. (ORNL)

Genetic screening 
Testing a group of people to identify individuals at high risk of having or passing on a specific genetic disorder. (ORNL)

Genetic testing 
Analyzing an individual's genetic material to determine predisposition to a particular health condition or to confirm a diagnosis of genetic disease. (ORNL)

The study of inheritance patterns of specific traits. (ORNL)

All the genetic material in the chromosomes of a particular organism; its size is generally given as its total number of base pairs. (ORNL)

Genome project 
Research and technology-development effort aimed at mapping and sequencing the genome of human beings and certain model organisms. 
See also: Human Genome Initiative (ORNL)

Genomic library 
A collection of clones made from a set of randomly generated overlapping DNA fragments that represent the entire genome of an organism. 
See also: libraryarrayed library (ORNL)

Genomic sequence 

The study of genes and their function. (ORNL)

The genetic constitution of an organism, as distinguished from its physical appearance (its phenotype). (ORNL)

Germ cell 
Sperm and egg cells and their precursors. Germ cells are haploid and have only one set of chromosomes (23 in all), while all other cells have two copies (46 in all). (ORNL)

Germ line 
The continuation of a set of genetic information from one generation to the next. 
See also: inherit (ORNL)

Germ line gene therapy 
An experimental process of inserting genes into germ cells or fertilized eggs to cause a genetic change that can be passed on to offspring. May be used to alleviate effects associated with a genetic disease. 
See also: genomicssomatic cell gene therapy. (ORNL)

Germ line genetic mutation 
See: mutation (ORNL)

Global Alignment 
The alignment of two nucleic acid or protein sequences over their entire length. (NCBI)

a topology for a small number of beta sheet strands in which some interstrand connections going across the end of barrel or, in a sandwich fold, between beta sheets. (SCOP)

Guanine (G) 
A nitrogenous base, one member of the base pair GC (guanine and cytosine) in DNA. 
See also: base pairnucleotide (ORNL)

H  [top]

H is the relative entropy of the target and background residue frequencies. (Karlin and Altschul, 1990). H can be thought of as a measure of the average information (in bits) available per position that distinguishes an alignment from chance. At high values of H, short alignments can be distinguished by chance, whereas at lower H values, a longer alignment may be necessary. (Altschul, 1991) (NCBI)

A single set of chromosomes (half the full set of genetic material) present in the egg and sperm cells of animals and in the egg and pollen cells of plants. Human beings have 23 chromosomes in their reproductive cells. 
See also: diploid (ORNL)

A way of denoting the collective genotype of a number of closely linked loci on a chromosome. (ORNL)

Having only one copy of a particular gene. For example, in humans, males are hemizygous for genes found on the Y chromosome. (ORNL)

Hereditary cancer 
Cancer that occurs due to the inheritance of an altered gene within a family. 
See also: sporadic cancer (ORNL)

The presence of different alleles at one or more loci on homologous chromosomes. (ORNL)

See: heterozygosity (ORNL)

Highly conserved sequence 
DNA sequence that is very similar across several different types of organisms. 
See also: genemutation (ORNL)

High-throughput sequencing 
A fast method of determining the order of bases in DNA. 
See also: sequencing (ORNL)

A short stretch of nucleotides whose base sequence is virtually identical in all the genes that contain it. Homeoboxes have been found in many organisms from fruit flies to human beings. In the fruit fly, a homeobox appears to determine when particular groups of genes are expressed during development. (ORNL)

A member of a chromosome pair in diploid organisms or a gene that has the same origin and functions in two or more species. (ORNL)

Homologous chromosome 
Chromosome containing the same linear gene sequences as another, each derived from one parent. (ORNL)

Homologous recombination 
Swapping of DNA fragments between paired chromosomes. (ORNL)

Similarity attributed to descent from a common ancestor. (NCBI)

Similarity in DNA or protein sequences between individuals of the same species or among different species. (ORNL)

Evolutionary descent from a common ancestor due to gene duplication. (SMART)

An organism that has two identical alleles of a gene. 
See also: heterozygote (ORNL)

See: homozygote (ORNL)

High-scoring segment pair. Local alignments with no gaps that achieve one of the top alignment scores in a given search. (NCBI)

Human gene therapy 
See: gene therapy (ORNL)

Human Genome Initiative 
Collective name for several projects begun in 1986 by DOE to create an ordered set of DNA segments from known chromosomal locations, develop new computational methods for analyzing genetic map and DNA sequence data, and develop new techniques and instruments for detecting and analyzing DNA. This DOE initiative is now known as the Human Genome Program. The joint national effort, led by DOE and NIH, is known as the Human Genome Project. (ORNL)

Human Genome Project (HGP) 
Formerly titled Human Genome Initiative. 
See also: Human Genome Initiative (ORNL)

The offspring of genetically different parents. 
See also: heterozygote (ORNL)

The process of joining two complementary strands of DNA or one each of DNA and RNA to form a double-stranded molecule. (ORNL)

I  [top]

Identical twin 
Twins produced by the division of a single zygote; both have identical genotypes. 
See also: fraternal twin (ORNL)

The extent to which two (nucleotide or amino acid) sequences are invariant. (NCBI)

Using the immune system to treat disease, for example, in the development of vaccines. May also refer to the therapy of diseases caused by the immune system. 
See also: cancer (ORNL)

A phenomenon in which the disease phenotype depends on which parent passed on the disease gene. For instance, both Prader-Willi and Angelman syndromes are inherited when the same part of chromosome 15 is missing. When the father's complement of 15 is missing, the child has Prader-Willi, but when the mother's complement of 15 is missing, the child has Angelman syndrome. (ORNL)

In situ hybridization 
Use of a DNA or RNA probe to detect the presence of the complementary DNA sequence in cloned bacterial or cultured eukaryotic cells. (ORNL)

In vitro 
Studies performed outside a living organism such as in a laboratory. (ORNL)

In vivo 
Studies carried out in living organisms. (ORNL)

Independent assortment 
During meiosis each of the two copies of a gene is distributed to the germ cells independently of the distribution of other genes. 
See also: linkage (ORNL)

See: bioinformatics (ORNL)

Informed consent 
An individual willingly agrees to participate in an activity after first being advised of the risks and benefits. 
See also: privacy (ORNL)

In genetics, to receive genetic material from parents through biological processes. (ORNL)

See: inherit (ORNL)

A chromosome abnormality in which a piece of DNA is incorporated into a gene and thereby disrupts the gene's normal function. 
See also: chromosomeDNAgenemutation (ORNL)

Insertional mutation 
See: insertion (ORNL)

Intellectual property rights 
Patents, copyrights, and trademarks. 
See also: patent (ORNL)

One crossover event inhibits the chances of another crossover event. Also known as positive interference. Negative interference increases the chance of a second crossover. 
See also: crossing over (ORNL)

The period in the cell cycle when DNA is replicated in the nucleus; followed by mitosis. (ORNL)

Intracellular Domains
Domain families that are most prevalent in proteins within the cytoplasm. (SMART)

DNA sequence that interrupts the protein-coding sequence of a gene; an intron is transcribed into RNA but is cut out of the message before it is translated into protein. 
See also: exon (ORNL)

An enzyme performing the same function as another enzyme but having a different set of amino acids. The two enzymes may function at different speeds. (ORNL)

J  [top]

A variant of Greek key topology with both ends of a sandwich or a barrel fold being crossed by two interstrand connections. (SCOP)

Junk DNA 
Stretches of DNA that do not code for genes; most of the genome consists of so-called junk DNA which may have regulatory and other functions. Also called non-coding DNA. (ORNL)

K  [top]

A statistical parameter used in calculating BLAST scores that can be thought of as a natural scale for search space size. The value K is used in converting a raw score (S) to a bit score (S'). (NCBI)

A photomicrograph of an individual's chromosomes arranged in a standard format showing the number, size, and shape of each chromosome type; used in low-resolution physical mapping to correlate gross chromosomal abnormalities with the characteristics of specific diseases. (ORNL)

Kilobase (kb) 
Unit of length for DNA fragments equal to 1000 nucleotides. (ORNL)

Deactivation of specific genes; used in laboratory organisms to study gene function. 
See also: genelocusmodel organisms (ORNL)

L  [top]

A statistical parameter used in calculating BLAST scores that can be thought of as a natural scale for scoring system. The value lambda is used in converting a raw score (S) to a bit score (S'). (NCBI)

An unordered collection of clones (i.e., cloned DNA from a particular organism) whose relationship to each other can be established by physical mapping. 
See also: genomic libraryarrayed library (ORNL)

The proximity of two or more markers (e.g., genes, RFLP markers) on a chromosome; the closer the markers, the lower the probability that they will be separated during DNA repair or replication processes (binary fission in prokaryotes, mitosis or meiosis in eukaryotes), and hence the greater the probability that they will be inherited together. (ORNL)

Linkage disequilibrium 
Where alleles occur together more often than can be accounted for by chance. Indicates that the two alleles are physically close on the DNA strand. 
See also: Mendelian inheritance (ORNL)

Linkage map 
A map of the relative positions of genetic loci on a chromosome, determined on the basis of how often the loci are inherited together. Distance is measured in centimorgans (cM). (ORNL)

Local Alignment 
The alignment of some portion of two nucleic acid or protein sequences (NCBI)

Numbers of domains that are thought from SwissProt annotations to be present in different cellular compartments (cytoplasm, extracellular space, nucleus, and membrane-associated) are shown in annotation pages. (SMART)

Determination of the original position (locus) of a gene or other marker on a chromosome. (ORNL)

Locus (pl. loci) 
The position on a chromosome of a gene or other chromosome marker; also, the DNA at that position. The use of locus is sometimes restricted to mean expressed DNA regions. 
See also: gene expression (ORNL)

Long-Range Restriction Mapping 
Restriction enzymes are proteins that cut DNA at precise locations. Restriction maps depict the chromosomal positions of restriction-enzyme cutting sites. These are used as biochemical "signposts," or markers of specific areas along the chromosomes. The map will detail the positions where the DNA molecule is cut by particular restriction enzymes. (ORNL)

Low Complexity Region (LCR) 
Regions of biased composition including homopolymeric runs, short-period repeats, and more subtle overrepresentation of one or a few residues. The SEG program is used to mask or filter LCRs in amino acid queries. The DUST program is used to mask or filter LCRs in nucleic acid queries. (NCBI)

M  [top]

Macrorestriction map 
Map depicting the order of and distance between sites at which restriction enzymes cleave chromosomes. (ORNL)

See: gene mappinglinkage mapphysical map (ORNL)

Mapping population 
The group of related organisms used in constructing a genetic map. (ORNL)

See: genetic marker (ORNL)

Also known as Filtering. The removal of repeated or low complexity regions from a sequence in order to improve the sensitivity of sequence similarity searches performed with that sequence. (NCBI)

Mass spectrometry 
An instrument used to identify chemicals in a substance by their mass and charge. (ORNL)

A simple topology of a beta-sheet where any two consecutive strands are adjacent and antiparallel (SCOP)

Megabase (Mb) 
Unit of length for DNA fragments equal to 1 million nucleotides and roughly equal to 1 cM. 
See also: centimorgan (ORNL)

The process of two consecutive cell divisions in the diploid progenitors of sex cells. Meiosis results in four rather than two daughter cells, each with a haploid set of chromosomes. 
See also: mitosis (ORNL)

Mendelian inheritance 
One method in which genetic traits are passed from parents to offspring. Named for Gregor Mendel, who first studied and recognized the existence of genes and this method of inheritance. 
See also: autosomal dominantrecessive genesex-linked (ORNL)

Messenger RNA (mRNA) 
RNA that serves as a template for protein synthesis. 
See also: genetic code (ORNL)

A stage in mitosis or meiosis during which the chromosomes are aligned along the equatorial plane of the cell. (ORNL)

Sets of miniaturized chemical reaction areas that may also be used to test DNA fragments, antibodies, or proteins. (ORNL)

Microbial genetics 
The study of genes and gene function in bacteria, archaea, and other microorganisms. Often used in research in the fields of bioremediation, alternative energy, and disease prevention. 
See also: model organismsbiotechnologybioremediation (ORNL)

A technique for introducing a solution of DNA into a cell using a fine microcapillary pipet. (ORNL)

Mitochondrial DNA 
The genetic material found in mitochondria, the organelles that generate energy for the cell. Not inherited in the same fashion as nucleic DNA. 
See also: cellDNAgenomenucleus(ORNL)

The process of nuclear division in cells that produces daughter cells that are genetically identical to each other and to the parent cell. 
See also: meiosis (ORNL)

Model organisms 
A laboratory animal or other organism useful for research. (ORNL)

The use of statistical analysis, computer analysis, or model organisms to predict outcomes of research. (ORNL)

Molecular biology 
The study of the structure, function, and makeup of biologically important molecules. (ORNL)

Molecular farming 
The development of transgenic animals to produce human proteins for medical use. (ORNL)

Molecular genetics 
The study of macromolecules important in biological inheritance. (ORNL)

Molecular medicine 
The treatment of injury or disease at the molecular level. Examples include the use of DNA-based diagnostic tests or medicine derived from DNA sequence information. (ORNL)

Monogenic disorder 
A disorder caused by mutation of a single gene. 
See also: mutationpolygenic disorder (ORNL)

Monogenic inheritance 
See: monogenic disorder (ORNL)

Possessing only one copy of a particular chromosome instead of the normal two copies. 
See also: cellchromosomegene expressiontrisomy (ORNL)

Morbid map 
A diagram showing the chromosomal location of genes associated with disease. (ORNL)

A short conserved region in a protein sequence. Motifs are frequently highly conserved parts of domains. (NCBI)

Sequence motifs are short conserved regions of polypeptides. Sets of sequence motifs need not necessarily represent homologues. (SMART)

Mouse model 
See: model organisms (ORNL)

Multifactorial or Multigenic Disorder 
See: polygenic disorder (ORNL)

Multiple Sequence Alignment 
An alignment of three or more sequences with gaps inserted in the sequences such that residues with common structural positions and/or ancestral residues are aligned in the same column. Clustal W is one of the most widely used multiple sequence alignment programs (NCBI)

A laboratory approach that performs multiple sets of reactions in parallel (simultaneously); greatly increasing speed and throughput. (ORNL)

Organism in the genus Mus. A rat or mouse. (ORNL)

An agent that causes a permanent genetic change in a cell. Does not include changes occurring during normal genetic recombination. (ORNL)

The capacity of a chemical or physical agent to cause permanent genetic alterations. 
See also: somatic cell genetic mutation (ORNL)

Any heritable change in DNA sequence. 
See also: polymorphism (ORNL)

N  [top]

Nitrogenous base 
A nitrogen-containing molecule having the chemical properties of a base. DNA contains the nitrogenous bases adenine (A), guanine (G), cytosine (C), and thymine (T). 
See also: DNA (ORNL)

Northern blot 
A gel-based laboratory procedure that locates mRNA sequences on a gel that are complementary to a piece of DNA used as a probe. 
See also: DNAlibrary (ORNL)

Nuclear transfer 
A laboratory procedure in which a cell's nucleus is removed and placed into an oocyte with its own nucleus removed so the genetic information from the donor nucleus controls the resulting cell. Such cells can be induced to form embryos. This process was used to create the cloned sheep "Dolly". 
See also: cloning (ORNL)

Nucleic acid 
A large molecule composed of nucleotide subunits. 
See also: DNA (ORNL)

Nucleolar organizing region 
A part of the chromosome containing rRNA genes. (ORNL)

A subunit of DNA or RNA consisting of a nitrogenous base (adenine, guanine, thymine, or cytosine in DNA; adenine, guanine, uracil, or cytosine in RNA), a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). Thousands of nucleotides are linked to form a DNA or RNA molecule. 
See also: DNAbase pairRNA (ORNL)

The cellular organelle in eukaryotes that contains most of the genetic material. (ORNL)

O  [top]

See: oligonucleotide (ORNL)

A phenotypic trait produced by two or more genes working together. 
See also: polygenic disorder (ORNL)

A molecule usually composed of 25 or fewer nucleotides; used as a DNA synthesis primer. 
See also: nucleotide (ORNL)

A gene, one or more forms of which is associated with cancer. Many oncogenes are involved, directly or indirectly, in controlling the rate of cell growth. (ORNL)

Open reading frame (ORF) 
The sequence of DNA or RNA located between the start-code sequence (initiation codon) and the stop-code sequence (termination codon). (ORNL)

A set of genes transcribed under the control of an operator gene. (ORNL)

Optimal Alignment 
An alignment of two sequences with the highest possible score. (NCBI)

Open reading frame. (SMART)

Homologous sequences in different species that arose from a common ancestral gene during speciation; may or may not be responsible for a similar function. (NCBI)

Overlapping clones 
See: genomic library (ORNL)

P  [top]

P value 
The probability of an alignment occurring with the score in question or better. The p value is calculated by relating the observed alignment score, S, to the expected distribution of HSP scores from comparisons of random sequences of the same length and composition as the query to the database. The most highly significant P values will be those close to 0. P values and E values are different ways of representing the significance of the alignment. (NCBI)

P1-derived artificial chromosome (PAC) 
One type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on bacteriophage (a virus) P1 genome. 
See also: cloning vector (ORNL)

Point Accepted Mutation. A unit introduced by Dayhoff et al. to quantify the amount of evolutionary change in a protein sequence. 1.0 PAM unit, is the amount of evolution which will change, on average, 1% of amino acids in a protein sequence. A PAM(x) substitution matrix is a look-up table in which scores for each amino acid substitution have been calculated based on the frequency of that substitution in closely related proteins that have experienced a certain amount (x) of evolutionary divergence. (NCBI)

Homologous sequences within a single species that arose by gene duplication. (NCBI)

Partly open barrel 
Has the edge strands not properly hydrogen bonded because one of the strands is in two parts connected with a linker of more than than one residue. These edge strands can be treated as a single but interrupted strand, allowing classification with the effective strand and shear numbers, n* and S*. In the few open barrels the beta sheets are connected by only a few side-chain hydrogen bonds between the edge strands. (SCOP)

In genetics, conferring the right or title to genes, gene variations, or identifiable portions of sequenced genetic material to an individual or organization. 
See also: gene (ORNL)

A family tree diagram that shows how a particular genetic trait or disease has been inherited. 
See also: inherit (ORNL)

The probability of a gene or genetic trait being expressed. "Complete" penetrance means the gene or genes for a trait are expressed in all the population who have the genes. "Incomplete" penetrance means the genetic trait is expressed in only part of the population. The percent penetrance also may change with the age range of the population. (ORNL)

Two or more amino acids joined by a bond called a "peptide bond." 
See also: polypeptide (ORNL)

A virus for which the natural host is a bacterial cell. (ORNL)

The study of the interaction of an individual's genetic makeup and response to a drug. (ORNL)

A trait not caused by inheritance of a gene but appears to be identical to a genetic trait. (ORNL)

The physical characteristics of an organism or the presence of a disease that may or may not be genetic. 
See also: genotype (ORNL)

Physical map 
A map of the locations of identifiable landmarks on DNA (e.g., restriction-enzyme cutting sites, genes), regardless of inheritance. Distance is measured in base pairs. For the human genome, the lowest-resolution physical map is the banding patterns on the 24 different chromosomes; the highest-resolution map is the complete nucleotide sequence of the chromosomes. (ORNL)

Autonomously replicating extra-chromosomal circular DNA molecules, distinct from the normal bacterial genome and nonessential for cell survival under nonselective conditions. Some plasmids are capable of integrating into the host genome. A number of artificially constructed plasmids are used as cloning vectors. (ORNL)

One gene that causes many different physical traits such as multiple disease symptoms. (ORNL)

The potential of a cell to develop into more than one type of mature cell, depending on environment. (ORNL)

Polygenic disorder 
Genetic disorder resulting from the combined action of alleles of more than one gene (e.g., heart disease, diabetes, and some cancers). Although such disorders are inherited, they depend on the simultaneous presence of several alleles; thus the hereditary patterns usually are more complex than those of single-gene disorders. 
See also: single-gene disorder (ORNL)

Polymerase chain reaction (PCR) 
A method for amplifying a DNA base sequence using a heat-stable polymerase and two 20-base primers, one complementary to the (+) strand at one end of the sequence to be amplified and one complementary to the (-) strand at the other end. Because the newly synthesized DNA strands can subsequently serve as additional templates for the same primer sequences, successive rounds of primer annealing, strand elongation, and dissociation produce rapid and highly specific amplification of the desired sequence. PCR also can be used to detect the existence of the defined sequence in a DNA sample. (ORNL)

Polymerase, DNA or RNA 
Enzyme that catalyzes the synthesis of nucleic acids on preexisting nucleic acid templates, assembling RNA from ribonucleotides or DNA from deoxyribonucleotides. (ORNL)

Difference in DNA sequence among individuals that may underlie differences in health. Genetic variations occurring in more than 1% of a population would be considered useful polymorphisms for genetic linkage analysis. 
See also: mutation (ORNL)

A protein or part of a protein made of a chain of amino acids joined by a peptide bond. (ORNL)

Population genetics 
The study of variation in genes among a group of individuals. (ORNL)

Positional cloning 
A technique used to identify genes, usually those that are associated with diseases, based on their location on a chromosome. (ORNL)

Short preexisting polynucleotide chain to which new deoxyribonucleotides can be added by DNA polymerase. (ORNL)

In genetics, the right of people to restrict access to their genetic information. (ORNL)

Single-stranded DNA or RNA molecules of specific base sequence, labeled either radioactively or immunologically, that are used to detect the complementary base sequence by hybridization. (ORNL)

A table that lists the frequencies of each amino acid in each position of protein sequence. Frequencies are calculated from multiple alignments of sequences containing a domain of interest. See also PSSM. (NCBI)

A profile is a table of position-specific scores and gap penalties, representing an homologous family, that may be used to search sequence databases. In CLUSTAL-W-derived profiles those sequences that are more distantly related are assigned higher weights. (SMART)

Cell or organism lacking a membrane-bound, structurally discrete nucleus and other subcellular compartments. Bacteria are examples of prokaryotes. 
See also: chromosomeeukaryote (ORNL)

A DNA site to which RNA polymerase will bind and initiate transcription. (ORNL)

The nucleus of a sperm or egg prior to fertilization. 
See also: nucleustransgenic (ORNL)

A large molecule composed of one or more chains of amino acids in a specific order; the order is determined by the base sequence of nucleotides in the gene that codes for the protein. Proteins are required for the structure, function, and regulation of the body's cells, tissues, and organs; and each protein has unique functions. Examples are hormones, enzymes, and antibodies. (ORNL)

Proteins expressed by a cell or organ at a particular time and under specific conditions. (ORNL)

Systematic analysis of protein expression of normal and diseased tissues that involves the separation, identification and characterization of all of the proteins in an organism. (NCBI)

A sequence of DNA similar to a gene but nonfunctional; probably the remnant of a once-functional gene that accumulated mutations. (ORNL)

Position-Specific Iterative BLAST. An iterative search using the BLAST algorithm. A profile is built after the initial search, which is then used in subsequent searches. The process may be repeated, if desired with new sequences found in each cycle used to refine the profile. Details can be found in this discussion of PSI-BLAST. (Altschul et al.) (NCBI)

Position-specific scoring matrix; see profile. The PSSM gives the log-odds score for finding a particular matching amino acid in a target sequence. (NCBI)

A nitrogen-containing, double-ring, basic compound that occurs in nucleic acids. The purines in DNA and RNA are adenine and guanine. 
See also: base pair (ORNL)

A nitrogen-containing, single-ring, basic compound that occurs in nucleic acids. The pyrimidines in DNA are cytosine and thymine; in RNA, cytosine and uracil. 
See also: base pair (ORNL)

Q  [top]

The input sequence (or other type of search term) with which all of the entries in a database are to be compared. (NCBI)

R  [top]

Radiation hybrid 
A hybrid cell containing small fragments of irradiated human chromosomes. Maps of irradiation sites on chromosomes for the human, rat, mouse, and other genomes provide important markers, allowing the construction of very precise STS maps indispensable to studying multifactorial diseases. 
See also: sequence tagged site (ORNL)

Rare-cutter enzyme 
See: restriction-enzyme cutting site (ORNL)

Raw Score 
The score of an alignment, S, calculated as the sum of substitution and gap scores. Substitution scores are given by a look-up table (see PAM, BLOSUM). Gap scores are typically calculated as the sum of G, the gap opening penalty and L, the gap extension penalty. For a gap of length n, the gap cost would be G+Ln. The choice of gap costs, G and L is empirical, but it is customary to choose a high value for G (10-15)and a low value for L (1-2). (NCBI)

Recessive gene 
A gene which will be expressed only if there are 2 identical copies or, for a male, if one copy is present on the X chromosome. (ORNL)

Reciprocal translocation 
When a pair of chromosomes exchange exactly the same length and area of DNA. Results in a shuffling of genes. (ORNL)

Recombinant clone 
Clone containing recombinant DNA molecules. 
See also: recombinant DNA technology (ORNL)

Recombinant DNA molecules 
A combination of DNA molecules of different origin that are joined using recombinant DNA technologies. (ORNL)

Recombinant DNA technology 
Procedure used to join together DNA segments in a cell-free system (an environment outside a cell or organism). Under appropriate conditions, a recombinant DNA molecule can enter a cell and replicate there, either autonomously or after it has become integrated into a cellular chromosome. (ORNL)

The process by which progeny derive a combination of genes different from that of either parent. In higher organisms, this can occur by crossing over. 
See also: crossing overmutation (ORNL)

Regulatory region or sequence 
A DNA base sequence that controls gene expression. (ORNL)

Repetitive DNA 
Sequences of varying lengths that occur in multiple copies in the genome; it represents much of the human genome. (ORNL)

Reporter gene 
See: marker (ORNL)

Degree of molecular detail on a physical map of DNA, ranging from low to high. (ORNL)

Restriction enzyme, endonuclease 
A protein that recognizes specific, short nucleotide sequences and cuts DNA at those sites. Bacteria contain over 400 such enzymes that recognize and cut more than 100 different DNA sequences. 
See also: restriction enzyme cutting site (ORNL)

Restriction fragment length polymorphism (RFLP) 
Variation between individuals in DNA fragment sizes cut by specific restriction enzymes; polymorphic sequences that result in RFLPs are used as markers on both physical maps and genetic linkage maps. RFLPs usually are caused by mutation at a cutting site. 
See also: markerpolymorphism (ORNL)

Restriction-enzyme cutting site 
A specific nucleotide sequence of DNA at which a particular restriction enzyme cuts the DNA. Some sites occur frequently in DNA (e.g., every several hundred base pairs); others much less frequently (rare-cutter; e.g., every 10,000 base pairs). (ORNL)

Retroviral infection 
The presence of retroviral vectors, such as some viruses, which use their recombinant DNA to insert their genetic material into the chromosomes of the host's cells. The virus is then propogated by the host cell. (ORNL)

Reverse transcriptase 
An enzyme used by retroviruses to form a complementary DNA sequence (cDNA) from their RNA. The resulting DNA is then inserted into the chromosome of the host cell. (ORNL)

See: nucleotide (ORNL)

The five-carbon sugar that serves as a component of RNA. 
See also: RNAdeoxyribose (ORNL)

Ribosomal RNA (rRNA) 
A class of RNA found in the ribosomes of cells. (ORNL)

Small cellular components composed of specialized ribosomal RNA and protein; site of protein synthesis. 
See also: RNA (ORNL)

Risk communication 
In genetics, a process in which a genetic counselor or other medical professional interprets genetic test results and advises patients of the consequences for them and their offspring. (ORNL)

RNA (Ribonucleic acid) 
A chemical found in the nucleus and cytoplasm of cells; it plays an important role in protein synthesis and other chemical activities of the cell. The structure of RNA is similar to that of DNA. There are several classes of RNA molecules, including messenger RNA, transfer RNA, ribosomal RNA, and other small RNAs, each serving a different purpose. (ORNL)

S  [top]

Sanger sequencing 
A widely used method of determining the order of bases in DNA. 
See also: sequencingshotgun sequencing (ORNL)

A chromosomal segment that branches off from the rest of the chromosome but is still connected by a thin filament or stalk. (ORNL)

In genomic mapping, a series of contigs that are in the right order but not necessarily connected in one continuous stretch of sequence. (ORNL)

Seed Alignment
Alignment that contains only one of each pair of homologues that are represented in a CLUSTALW-derived phylogenetic tree linked by a branch of length less than a distance of 0.2 (see the related article). (SMART)

A program for filtering low complexity regions in amino acid sequences. Residues that have been masked are represented as "X" in an alignment. SEG filtering is performed by default in the blastp subroutine of BLAST 2.0. (Wootton and Federhen) (NCBI)

The normal biological process whereby the two pieces of a chromosome pair are separated during meiosis and randomly distributed to the germ cells. (ORNL)

See: base sequence (ORNL)

Sequence assembly 
A process whereby the order of multiple sequenced DNA fragments is determined. (ORNL)

Sequence tagged site (STS) 
Short (200 to 500 base pairs) DNA sequence that has a single occurrence in the human genome and whose location and base sequence are known. Detectable by polymerase chain reaction, STSs are useful for localizing and orienting the mapping and sequence data reported from many different laboratories and serve as landmarks on the developing physical map of the human genome. Expressed sequence tags (ESTs) are STSs derived from cDNAs. (ORNL)

Determination of the order of nucleotides (base sequences) in a DNA or RNA molecule or the order of amino acids in a protein. (ORNL)

Sequencing technology 
The instrumentation and procedures used to determine the order of nucleotides in DNA. (ORNL)

Sex chromosome 
The X or Y chromosome in human beings that determines the sex of an individual. Females have two X chromosomes in diploid cells; males have an X and a Y chromosome. The sex chromosomes comprise the 23rd chromosome pair in a karyotype. 
See also: autosome (ORNL)

Traits or diseases associated with the X or Y chromosome; generally seen in males. 
See also: genemutationsex chromosome (ORNL)

Shotgun method 
Sequencing method that involves randomly sequenced cloned pieces of the genome, with no foreknowledge of where the piece originally came from. This can be contrasted with "directed" strategies, in which pieces of DNA from known chromosomal locations are sequenced. Because there are advantages to both strategies, researchers use both random (or shotgun) and directed strategies in combination to sequence the human genome. 
See also: librarygenomic library (ORNL)

The extent to which nucleotide or protein sequences are related. The extent of similarity between two sequences can be based on percent sequence identity and/or conservation. In BLAST similarity refers to a positive matrix score. (NCBI)

Single nucleotide polymorphism (SNP) 
DNA sequence variations that occur when a single nucleotide (A, T, C, or G) in the genome sequence is altered. 
See also: mutationpolymorphismsingle-gene disorder (ORNL)

Single-gene disorder 
Hereditary disorder caused by a mutant allele of a single gene (e.g., Duchenne muscular dystrophy, retinoblastoma, sickle cell disease). 
See also: polygenic disorders (ORNL)

Somatic cell 
Any cell in the body except gametes and their precursors. 
See also: gamete (ORNL)

Somatic cell gene therapy 
Incorporating new genetic material into cells for therapeutic purposes. The new genetic material cannot be passed to offspring. 
See also: gene therapy (ORNL)

Somatic cell genetic mutation 
A change in the genetic structure that is neither inherited nor passed to offspring. Also called acquired mutations. 
See also: germ line genetic mutation (ORNL)

Southern blotting 
Transfer by absorption of DNA fragments separated in electrophoretic gels to membrane filters for detection of specific base sequences by radio-labeled complementary probes. (ORNL)

Spectral karyotype (SKY) 
A graphic of all an organism's chromosomes, each labeled with a different color. Useful for identifying chromosomal abnormalities. 
See also: chromosome (ORNL)

Splice site 
Location in the DNA sequence where RNA removes the noncoding areas to form a continuous gene transcript for translation into a protein. (ORNL)

Sporadic cancer 
Cancer that occurs randomly and is not inherited from parents. Caused by DNA changes in one cell that grows and divides, spreading throughout the body. 
See also: hereditary cancer (ORNL)

Stem cell 
Undifferentiated, primitive cells in the bone marrow that have the ability both to multiply and to differentiate into specific blood cells. (ORNL)

Structural genomics 
The effort to determine the 3D structures of large numbers of proteins using both experimental techniques and computer simulation (ORNL)

The presence of a non-identical amino acid at a given position in an alignment. If the aligned residues have similar physico-chemical properties the substitution is said to be "conservative". (NCBI)

In genetics, a type of mutation due to replacement of one nucleotide in a DNA sequence by another nucleotide or replacement of one amino acid in a protein by another amino acid. 
See also: mutation (ORNL)

Substitution Matrix 
A substitution matrix containing values proportional to the probability that amino acid i mutates into amino acid j for all pairs of amino acids. such matrices are constructed by assembling a large and diverse sample of verified pairwise alignments of amino acids. If the sample is large enough to be statistically significant, the resulting matrices should reflect the true probabilities of mutations occuring through a period of evolution. (NCBI)

Suppressor gene 
A gene that can suppress the action of another gene. (ORNL)

The group or recognizable pattern of symptoms or abnormalities that indicate a particular trait or disease. (ORNL)

Genetically identical members of the same species. (ORNL)

Genes occurring in the same order on chromosomes of different species. 
See also: linkageconserved sequence (ORNL)

T  [top]

Tandem repeat sequences 
Multiple copies of the same base sequence on a chromosome; used as markers in physical mapping. 
See also: physical map (ORNL)

Targeted mutagenesis 
Deliberate change in the genetic structure directed at a specific site on the chromosome. Used in research to determine the targeted region's function. 
See also: mutationpolymorphism (ORNL)

Technology transfer 
The process of transferring scientific findings from research laboratories to the commercial sector. (ORNL)

The enzyme that directs the replication of telomeres. (ORNL)

The end of a chromosome. This specialized structure is involved in the replication and stability of linear DNA molecules. 
See also: DNA replication (ORNL)

Substances such as chemicals or radiation that cause abnormal development of a embryo. 
See also: mutatgen (ORNL)

Thymine (T) 
A nitrogenous base, one member of the base pair AT (adenine-thymine). 
See also: base pairnucleotide (ORNL)

The study of how genomes respond to environmental stressors or toxicants. Combines genome-wide mRNA expression profiling with protein expression patterns using bioinformatics to understand the role of gene-environment interactions in disease and dysfunction. (ORNL)

The synthesis of an RNA copy from a sequence of DNA (a gene); the first step in gene expression. 
See also: translation (ORNL)

Transcription factor 
A protein that binds to regulatory regions and helps control gene expression. (ORNL)

The full complement of activated genes, mRNAs, or transcripts in a particular tissue at a particular time (ORNL)

The introduction of foreign DNA into a host cell. 
See also: cloning vectorgene therapy (ORNL)

Transfer RNA (tRNA) 
A class of RNA having structures with triplet nucleotide sequences that are complementary to the triplet nucleotide coding sequences of mRNA. The role of tRNAs in protein synthesis is to bond with amino acids and transfer them to the ribosomes, where proteins are assembled according to the genetic code carried by mRNA. (ORNL)

A process by which the genetic material carried by an individual cell is altered by incorporation of exogenous DNA into its genome. (ORNL)

An experimentally produced organism in which DNA has been artificially introduced and incorporated into the organism's germ line. 
See also: cellDNAgenenucleusgerm line (ORNL)

The process in which the genetic code carried by mRNA directs the synthesis of proteins from amino acids. 
See also: transcription (ORNL)

A mutation in which a large segment of one chromosome breaks off and attaches to another chromosome. 
See also: mutation (ORNL)

Transposable element 
A class of DNA sequences that can move from one chromosomal site to another. (ORNL)

Possessing three copies of a particular chromosome instead of the normal two copies. 
See also: cellgenegene expressionchromosome (ORNL)

U  [top]

Unitary Matrix 
Also known as Identity Matrix. A scoring system in which only identical characters receive a positive score. (NCBI)

the simplest topology for a helical bundle or folded leaf, in which consecutive helices are adjacent and antiparallel; it is approximately equivalent to the meander topology of a beta-sheet. (SCOP)

A nitrogenous base normally found in RNA but not DNA; uracil is capable of forming a base pair with adenine. 
See also: base pairnucleotide (ORNL)

V  [top]

See: cloning vector (ORNL)

A noncellular biological entity that can reproduce only within a host cell. Viruses consist of nucleic acid covered by protein; some animal viruses are also surrounded by membrane. Inside the infected cell, the virus uses the synthetic capability of the host to produce progeny virus. 
See also: cloning vector (ORNL)

W  [top]

Western blot 
A technique used to identify and locate proteins based on their ability to bind to specific antibodies. 
See also: DNANorthern blotproteinRNASouthern blotting (ORNL)

Wild type 
The form of an organism that occurs most frequently in nature. (ORNL)

Working Draft DNA Sequence 
See: Draft DNA Sequence (ORNL)

X  [top]

X chromosome 
One of the two sex chromosomes, X and Y. 
See also: Y chromosomesex chromosome (ORNL)

Tissue or organs from an individual of one species transplanted into or grafted onto an organism of another species, genus, or family. A common example is the use of pig heart valves in humans. (ORNL)

Y  [top]

Y chromosome 
One of the two sex chromosomes, X and Y. 
See also: X chromosomesex chromosome (ORNL)

Yeast artificial chromosome (YAC) 
Constructed from yeast DNA, it is a vector used to clone large DNA fragments. 
See also: cloning vectorcosmid (ORNL)

Z  [top]

Zinc-finger protein 
A secondary feature of some proteins containing a zinc atom; a DNA-binding protein. (ORNL)


Sources for glossary:

RNA glossary from Cambridge Healthtech Institute
Glossary of Biotechnology Terms
Glossary of structural genomics
Genome Glossary (Oak Ridge National Laboratory)
The National Human Genome Research Institute (NHGRI), Talking Glossary of Genetic Terms
BLAST glossary from NCBI
Genomics Glossary from Cambridge Healthtech Institute
Multilingual Medical Terms
The Dictionary of Cell & Molecular Biology
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