Bioinformatics Glossary

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Trace

 A series of coloured peaks from which the individual bases of a sequence are derived. The original format is produced by the ABI Analysis software. This format is converted to SCF for use by xgap, by the Squirrel program. 

Tentative Consensus (TC)

The identification of a sequence from an EST cluster that represents part or all of a complete gene.  TCs are usually determined by clustering ESTs allowing for sequencing errors, artefacts such as chimeric clones, and naturally occuring biological phenomena such as alternative splicing.  Creation of a cluster allows one to generate a consensus sequence and then identify a long open reading frame which would suggest the possibility of that consensus representing a bona fide gene. 

Tentative Human Consensus sequences (THCs)

A consensus sequence generated from human EST fragments. THCs may be validated by comparison against databases of known human gene sequences, human genomic sequences, or by identification of the ORFs or other sequence features contained within the consensus as belonging to a known human gene product. 

Tertiary structure

Folding of a protein chain via interactions of its sideschain molecules including formation of disulfide bonds between cysteline residues. 

Thymine

A pyrimidine base found in DNA but not in RNA. 

Tissue

Section of an organ that consists of a largely homogenous population of cell types. Since many organs are multifunctional, they have developed highly specialized cell types to perform different functions. Identifying the section of an organ that is homogenous for a particular cell type ensures that the gene expression profiles extracted from those cells will accurately resemble the class of cells that make up the tissue. 

Transcript

The single-stranded mRNA chain that is assembled from a gene template. 

Transcription

The assembly of complementary single-stranded RNA on a DNA template.

Transcription factors

A group of regulatory proteins that are required for transcription in eukaryotes. Transcription factors bind to the promoter region of a gene and facilitate transcription by RNA polymerase. 

Transfer RNA (tRNA)

A small RNA molecule that recognizes a specific amino acid, transports it to a specific codon in the mRNA, and positions it properly in the nascent polypeptide chain. 

Transformation

A genetic alteration to a cell as a result of the incorporation of DNA from a genetically diferent cell or virus; can also refer to the introduction of DNA into bacterial cells for genetic manipulation. 

Transgene

A foreign gene that is introduced into a cell or whole organism (eg.transgenic mice) for therapeutic or experimental purposes. 

Translation

The process of converting RNA to protein by the assembly of a polypeptide chain from an mRNA molecule at the ribosome. 

Transmembrane region

The region of a transmembrane protein that actually spans the membrane.  Transmembrane regions are usually hydrophobic in order to be thermodynamically compatible with the lipid bilayer portion of the membrane.  They may consist of either alpha-helical or beta-strand secondary structure elements, but in either case the external residues (the ones facing the membrane) are invariably hydrophobic while the internal residues may be hydrophilic (as in the case of a pore or channel) or polar.  One common transmembrane structural domain is the seven-helix bundle seen in numerous channel proteins. 

(Continued on next part...)

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