C	C	Cytosine if in DNA, Cysteine if in protein.
	cc	C language compiler.
	C++	Object oriented C language compiler.
	capping	The modification of the 5' end of pre-mRNA in eukaryotes whereby a GTP is added to the molecule via a 5'-5' triphosphate bond.
	cap site	In the DNA, the site where transcription starts. In the RNA, the site that is capped during the process of mRNA maturation.
	carboxy terminal	The COOH end of a polypeptide.
	carrying capacity	The maximum number of individuals of a given species that can be sustained in a defined habitat.
	catalyst	A compound that lowers the energy necessary to activate a chemical reaction without being consumed or altered by it. Proteins are the primary catalysts in the cell, but RNA can act as a catalyst as well.
	cDNA	DNA that is synthesized from a messenger RNA template; the single stranded form is often used as a probe in physical mapping.
	cell	The basic structural units of life.
	centimorgan	100 Morgans. 100 million base pairs of DNA. Each "Morgan" is a length of genomic DNA equivalent to 1 million base pairs.
	central dogma	The path of information flow in DNA organisms (DNA -> RNA -> proteins).
	centromere	A specialized chromosome region to which spindle fibers attach during cell division.
	chaperonin	A multisubunit protein that forms a structure that aids the folding of other proteins.
	characters and character states	In phylogenetics, characters are homologous features in different organisms.
	chimera	An organism composed of two or more genetically different cell types.
	chimeric protein	A recombinant protein made up of two different proteins.
	chi site	A repeated nucleotide sequence in the E. coli genome that is involved in the initiation of homologous recombination.
	chloroplast	On of the photosynthetic organelles of a eukaryotic cell.
	Chromosomes	The self-replicating genetic structures 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 usually carried on one chromosome. Eukaryotic genomes consist of a number of chromosomes whose DNA is associated with different kinds of proteins.
	chromosome walking	A technique that can be used to construct a clone contig by identifying overlapping fragments of cloned DNA.
	chromatid	Each of the two copies produced by chromosome replication, or each of the two DNA strands that comprise the chromosome.
	CHARMM	A type of molecular mechanics force field used to predict the 3D structure of proteins.
	cis	The arrangement of two sequences or genes on the same chromosome.
	clade	According to the rigorous definition, a taxon consisting of a single species and all its descendants representing a monophyletic branch on an evolutionary tree. In looser usage, as above, except some descendants are not represented. In reference to extant organisms, a subgroup of organisms from among a larger group under consideration sharing a common ancestor not shared by the other organisms in the group.
	cladistics	A particular systematic approach to building evolutionary trees and interpreting their meaning. The cladistic approach attempts to reconstruct the branching pattern (order) of the evolutionary tree, but not estimate the passage of time on any particular branch.
	cladogenesis	Speciation
	cladogram	A graphic representation that portrays or attempts to portray the evolutionary relationships among a number of populations, species, or higher taxa.
	client	A computer, or the software running on a computer, that interacts with another computer at a remote site (server). In the X-window world, the client sits on the remote machine, and the X server sits on your local terminal.
	Clone	A collection of genetically identical copies of a gene, cell, or organism.
	Clone Bank	Genomic Library
	clone contig	A collection of clones whose DNA fragments overlap.
	Cloning	The process of asexually producing genetically identical copies of a gene, cell or organism (clone), all genetically identical, from a single ancestor. In recombinant DNA technology, the use of DNA manipulation procedures to produce multiple copies of a single gene or segment of DNA is referred to as cloning DNA.
	Cloning vector	DNA molecule originating from a virus, 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 it 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
	closed circular DNA	A DNA molecule that has no free 5' or 3' ends. Plasmids and certain viral DNA molecules have this structure.
	Cluster analysis	A process of assigning data points (sequences) into groups (clusters), starting from pairwise distances. Useful for identifying outliers and weak links between groups.
	coding region	All exon parts of a protein-coding gene that are ultimately translated.
	codominance	The equal contribution to fitness made by the two alleles at a locus in a diploid organism.
	codon	A triplet of nucleotides that is part of the genetic code and specifies the particular amino acid to be added to a growing chain to make a protein.
	codon family	All the codons that code for the same amino acid and differ from each other only at the third position. (e.g. among the six codons for leucine, UUA and UUG form one family, and CUU, CUC, CUA and CUG form another).
	codon preference, codon bias	The preferred codon usage in highly expressed genes.
	codon usage	The observed usage of the amino acid codons in a particular gene, tissue, or organism.
	coenzyme	An organic nonprotein molecule that does not bind the enzyme but is required for the function of the enzyme by acting as an intermediate carrier of electrons, atoms, or groups of atoms.
	cofactor	An inorganic molecule required by an enzyme in order to function.
	cohesive end	An end of a double-stranded DNA molecule where there is a single-stranded extension.
	coincidental evolution	Concerted evolution
	coincidental substitution	The occurrence of two substitutions at the same nucleotide site in two homologous sequences.
	collinearity	The exact correspondence between the DNA sequence of intronless genes and the amino acid sequence of the encoded protein
	collagen	The most abundant protein in mammals. An extracellular, rod-shaped, protein containing three helical polypeptide chains, each nearly 1000 residues in length.
	collagenase	An enzyme that degrades collagen.
	CoMFA	Comparative molecular field analysis - used for exploring structure activity relationships between proteins and ligands.
	Command line	Interacting with software by typing specific commands. Less "user friendly" but often more powerful because commands can be linked together and run automatically.
	Comparative genomics	The study of comparing complete genome sequences, often by computational methods, to understand general principles of genome structure and function.
	compiler	a program that performs the translation between a higher-level language (C, FORTRAN, Pascal) whose commands the computer cannot directly understand and a machine language file that the computer can run.
	complementary DNA (cDNA)	DNA that is synthesized from a messenger RNA template. The single-stranded form is often used as a probe in physical mapping.
	complex transpsoson	A transposon flanked by two complete, independently transposable insertion sequences.
	compositional assimilation	The accumulation of point mutations in a pseudogene that eventually obliterates its sequence similarity to the functional gene from which it has been derived and makes its nucleotide composition similar to neighboring DNA sequences.
	concatamer	A DNA molecule made up of linear genomes, linked head-to-tail.
	concerted evolution	Maintenance of homogeneity of nucleotide sequences among members of a gene family in a species, although the nucleotide sequences change over time.
	CONCORD	A software program that calculates the 3D structure of small molecules.
	Conditional fixation time	The time until fixation of a mutant allele that will eventually become fixed in the population.
	conditional-lethal mutation	A mutation that results in a cell or organism able to survive only under permissive conditions.
	conjugation	transfer of DNA between two bacteria which come into physical contact with one another.
	conjugation mapping	A technique for mapping bacterial genes by determining the time it takes for each gene to be transferred during conjugation.
	Conservative tranposition	The movement of a transposable element from one genomic position ot another without replication of the element.
	consensus sequence	A sequence thaty represents the most prevalent nucleotide or amino acid at each site in a number of aligned sequences. The consensus sequence character is often the residue that is the plurality at any position. However, a weight matrix is a more informative way to represent a group of sequences.
	conserved sequence	A base sequence in a DNA molecule (or an amino acid sequence in a protein) that has remained essentially unchanged throughout evolution.
	conservative substitution	The substitution of an amino acid by another with similar chemical properties.
	constitutive heterochromatin	Chromatin that is permanently in a compact organization.
	constituitive mutation	A mutation that results in continuous expression of a gene or set of genes that is normally subject to regulatory control.
	contigs	Groups of clones representing overlapping regions of a genome. DNA sequence read from several separate gels that has been merged or "assembled" into a longer contiguous segment.
	controlled vocabulary	A vocabulary that contains specific words that are consistently applied to all entries in a database. The MeSH system is an example of a controlled vocabulary.
	conventional pseudogene	A gene that has become inactive because of the accumulation of mutations.
	convergence	The independent evolution of similar genetic ro phenotypic traits.
	convergent substitution	The substitution of two different nucleotides by the same nucleotide at the same nucleotide site in two homologous sequences.
	CORBA	Common Object Request Broker Architecture, is a distributed object architecture that allows objects to interoperate across networks regardless of the language in which they were written or the platform on which they are deployed.
	cosmid	An artificaally constructed cloning vector capable of holding inserts of lengths aroudn 40,000 bases.
	CpG islands	A GC-rich DNA region located upstream of approximately 56% of the genes in the human genome. Tends to be antigenic.
	CPK Models	A style of displaying 3D protein structures in a space filling models, where oxygen is colored red, nitrogen is blue, carbon is black, hydrogen is white.
	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. Compare with recombination.
	cryptic splice site	A site whose sequence resembles an authentic splice site and which migh tbe selected instead of the authentic site during aberrant splicing.
	cryptogene	One of several genes in the trypanosome mitochondrial genome which specify abbreviated RNAs that must under go pan-editin in order to become functional.
	crystal	Solids that are exact repeats of a symmetric motif. In crystallography, a stacking of unit cells repeated in three dimensions to build a lattice, leaving no space between the unit cells.
	csh	The C shell. In UNIX, an environment where you can issue commands to the kernel. At the most basic level, the UNIX operating system is composed of a kernel and a shell.
	C-terminal	Carboxy (COOH) end of a protein
	C Value	The characteristic amount of DNA in the haploid genome of a species
	C Value Paradox	The apparent lack of correlation between teh C value and the level of morphological complexity
	Cyanobacteria	A type of photosynthetic eubacteria possessin the ability to phothsynthesize. Formerly called blue-green algae.
	cyclin	A regulatory protein whose abundance varies during the cell cycle and which reegulates biochemical events in a cell cycle-specific manner.
	Cytosine	A nitrogenous base in DNA and RNA. One member of the base pair G-C (guanine and cytosine).