A	A	Adenine if in DNA, Alanine if in protein.
	ab initio	From first principles. Deriving a 3D structure from initial physical forces and interactions.
	acceptor site	The 3' end of an intron
	accessible surface	The surface that is traced by the center of a probe molecule (usually water) as it rolls on the van der Waals surface of a molecule. The center of the probe molecule can be placed at any point on the accessible surface and not penetrate the van der Waals spheres of any of the atoms in the molecule.
	active site	A specific region of an enzyme where the substrate binds.
	additive tree	A phylogenetic tree in which the distance between any two terminal nodes is equal to the sum of the branch length connecting them.
	advantageous mutation	A mutation that increases the fitness of the organism carrying it.
	affine gap costs	A scoring system for gaps within alignments that charges a penalty for the existence of a gap and additional per-residue penalty proportional to the gap's length.
	agonist	A molecule that produces the same or elevated effect as the natural substrate or effector molecule (opposite of antagonist).
	algorithm	Any sequence of actions (computational steps) that perform a specific task.
	alignment	A one-to-one matching of two sequences so that each character in a pair of sequences is associated with a single character of the other sequence or with a gap.
	alignment score	A numerical value that describes the overall quality of an alignment. Higher numbers correspond to higher similarity.
	allele	One of two or more forms that a sequence of DNA (locus) can take. A single allele for each locus is inherited separately from each parent.
	alias	An abbreviation for a frequently used command or series of commands.
	alpha helix	Helical structure in a protein. A common secondary structure in proteins. (spectrin 2SPC)
	alternative splicing	The production of two or more mRNA molecules from a single pre-mRNA sequence by using different acceptor and donor sites.
	AMBER	A type of molecular mechanics force field used to predict the 3D structure of a protein.
	amber mutation	Mutation of the UAG (termination) codon.
	amino terminal	The -NH2 end of a polypeptide
	amino acid	Molecules that form the building blocks of proteins. There are twenty common amino acids found in proteins. Each amino acid is coded in DNA by a "codon"
	amino acid alphabet	A twenty-character alphabet, consisting of the characters A,C,D,E,F,G,H,I,K,L,M,N,P,P,R,S,T,V,W,Y, each representing one of the twenty amino acids coded for by DNA.
	amino acid substitution matrix	A matrix specifying the scores to use for character-specific matches and mismatches. The two most widely used matrices are the PAM and BLOSUM matrices.
	amphiphilic	of, relating to, or being a compound (as a surfactant) consisting of molecules having a polar water-soluble group attached to a water-insoluble hydrocarbon chain; also being a molecule of such a compound. Phospholipids in membranes are amphiphilic. (the opposite is amphipathic)
	amplification	An increase in the number of copies of a specific DNA fragment (beyond what is normal for the organisms haploid genome) ; can be in vivo or in vitro.
	analogy	Similarity by convergent evolution, but not by common evolutionary ancestry.
	aneuplody	The presence of extra chromosomes, such that the chromosomal composition of a cell is not an exact multiple of the haploid set.
	ancestral character state	A character state possessed by a remote common ancestor of a group of organisms.
	annealing	Attachment of an oligonucleotide primer to a DNA or RNA template.
	anticodon	A triplet of nucleotides in a tRNA molecule that associates by base pairing with a specific codon in the mRNA during translation and specifies the placement of a specific amino acid during translation.
	antigenic index	A prediction of the antigenicity of a sequence based on the hydrophilicity, predicted side chain flexibility, surface probability, and the predicted turns.
	antiparallel	The opposite orientation of the two complementary strands of a DNA duplex. The opposite orientation of two beta strands to create a beta sheet.
	apoprotein	A protein without its coenzymes, cofactors and prosthetic groups that are required for its functionality.
	archaebacteria	Prokaryotes that do not incorporate muramic acid into their cell walls. A highly diverse group of bacteria living at environmental extremes that represent one of the three taxonomic kingdoms.
	arithmetic mean	The sum of n terms divided by n.
	array	In the C (and other) programming languages, it is an ordered collection of data values, each of which is the same type.
	ASCII	American Standard Code for Information Interchange. The coding system used to represent characters, where each character that can be used by the computer is described by a unique numeric code.
	ASN.1	Abstract Syntax Notation number One (ASN.1) is an international standard that aims at specifying data used in communication protocols. It is a powerful and complex language: its features are designed to describe accurately and efficiently communications between homogeneous or heterogeneous systems.
	assembly	The process of correctly joining together the DNA sequences from individual sequencing experiments into a contiguous segment.
	asymmetrical exon	An exon flanked by introns of different phase classes.
	asymmetric unit	In a crystal, the level at which there is no symmetry. For example, the alpha-beta dimer can be considered to be the asymmetric unit of the hemoglobin tetramer in solution.
	attenuation	A process used by some bacteria to regulate expression of an amino acid biosynthetic operon in accordance with the levels of the amino acid in the cell.
	AU-AC intron	A type of intron found in eukaryotic nuclear genes: the first two nucleotides in the intron are 5'-AU-3' and the last two are 5'-AC-3'.
	Autonomously replicating sequence	A DNA sequence, especially from yeast, that confers replicative ability on a nonreplicative plasmid.
	autoradiography	The detection of radioactively labeled molecules by exposure of an X-ray sensitive photographic film.
	auxotroph	A mutant microorganism that can grow only when supplied with a nutrient that is not needed by the wild type.
	autosome	Any chromosome other than a sex chromosome. A chromosome not involved in sex determination. The diploid human genome consists of 46 chromosomes, 22 pairs of autosomes, and one pair of sex chromosomes (the X and the Y chromosomes).
	awk	A pattern scanning and processing language for UNIX. It searches one or more specified files, checking for records that match a specified pattern. If awk finds a match, the corresponding action is performed.