Bioinformatics glossary – K

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K is the single-letter amino acid code for Lysine.

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)

Statistical theory based on the extreme value distribution of the best scores for pairs of sequences; used for E-value calculation in BLAST.

Kaposi’s sarcoma (KS) is a rare type of cancer that develops from cells called endothelial cells. KS growths are called lesions or tumours. External lesions on the skin are the most common. But it can also involve internal organs such as the lymph nodes, lung, bowel, liver and spleen.

The inhibitory constant (Ki) describes the concentration of the inhibitor that is required in order to decrease the maximal rate of the reaction by half. Therefore, a small Ki value means that a lower concentration of a specific drug is needed to inhibit the activity of its target enzyme.

A two parameter substitution model used in phylogenetic studies in which transitions and transversions are considered.

Unit of length for DNA fragments equal to 1000 nucleotides

A kinase is in general an enzyme that catalyses the transfer of a phosphate

group from ATP to something else. In molecular biology, it has acquired the more specific

verbal usage for the transfer onto DNA of a radiolabelled phosphate group. This would be

done in order to use the resultant “hot” DNA as a probe.

A technique for deleting, mutating or otherwise inactivating a gene in a mouse. This laborious method involves transfecting a crippled gene into cultured embryonic stem cells, searching through the thousands of resulting clones for one in which the crippled gene exactly replaced the normal one (by homologous recombination), and inserting that cell back into a mouse blastocyst. The resulting mouse will be chimeric but, if you are lucky, its germ cells will carry the deleted gene. A few rounds of careful breeding can then produce progeny in which both copies of the gene are inactivated.

Change this value to limit the word-length the a Fasta search should use.