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Bioinformatics Glossary

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Accession number: An identifier supplied by the curators of the major biological databases upon submission of a novel entry that uniquely identifies that sequence (or other) entry. 

Active site:The amino acid residues at the catalytic site of an enzyme. These residues provide the binding and activation energy needed to place the substrate into its transition state and bridge the energy barrier of the reaction undergoing catalysis 

Adenine: A purine base found in DNA and RNA 

Agents: Independent, autonomous, software modules that can search the Internet for data or content pertinent to a particular application, such as a gene, protein, or biological system. 

Algorithm: A series of steps defining a procedure or formula for solving a problem, that can be coded into a programming language and executed. Bioinformatics algorithms typically are used to process, store, analyze, visualize and make predictions from biological data. 

Alignment: The result of a comparison of two or more gene or protein sequences in order to determine their degree of base or amino acid similarity. Sequence alignments are used to determine the similarity, homology, function or other degree of relatedness between two or more genes or gene products. 

Allele: A given form of a gene that occupies a specific position or locus on a chromosome. Variant forms of genes occurring at the same locus are said to be alleles of one another. 

Alternative splicing: One of the alternate combinations of a folded protein that are possible due to by recombination of multiple gene segments during mRNA splicing that occurs in higher organisms. 

Alternative splice-form: One of the possible alternate combinations of exons into a folded protein that are possible by recombining multiple gene segments during mRNA splicing in higher organisms. 

Alu family: A common set of dispersed DNA sequences found throughout the human genome; each is about 300 bases long and they are repeated at least 500,000 times. Alu sequences are speculated to have originated from viral RNA sequences that integrated into human DNA thousands of years ago. 

Amino acid: One of the 20 chemical building blocks that are joined by amide (peptide) linkages to form a polypeptide chain of a protein 

Analogy: Reasoning by which the function of a novel gene or protein sequence may be deduced from comparisons with other gene or protein sequences of known function.  Identifying analogous or homologous genes via similarity searching and alignment is one of the chief uses of Bioinformatics. (See also alignment, similarity search.) 

Annotation: A combination of comments, notations, references, and citations, either in free format or utilizing a controlled vocabulary, that together describe all the experimental and inferred information about a gene or protein.  Annotations can also be applied to the description of other biological systems.  Batch, automated annotation of bulk biological sequence is one of the key uses of Bioinformatics tools. 

Anticodon: The triplet of contiguous bases on tRNA that binds to the codon sequence of nucleotides on mRNA. Example: The codon for Glycine is GGG. The anticodon for Glycine is CCC. 

Antigen: Any foreign molecule that stimulates an immune response in a vertebrate organism. Many antigens are proteins such as the surface proteins of foreign organisms. 

Antisense: DNA or RNA composed of the complementary sequence to the target DNA/RNA. Also used to describe a therapeutic strategy that uses antisense DNA or RNA sequences to target specific gene DNA sequences or mRNA implicated in disease, in order to bind and physically inhibit their expression by physically blocking them. 

Assembly: Compilation of overlapping sequences from one or more related genes that have been clustered together based on their degree of sequence identity or similarity. Sequence assembly may be used to piece together "shotgun" sequencing fragments (see shotgun sequencing) based upon overlapping restriction enzyme digests, or may be used to identify and index novel genes from "single-pass" cDNA sequencing efforts. 

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