BPS 4104 Lecture Notes - Lecture 1: Expressed Sequence Tag, Sequence Database, Binomial Distribution
27 Mar 2018
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Early applications: sequence similarity between an oncogene (genes in viruses that cause a cancer-like transformation of the infected cells), v-sis, and the platelet-derived growth factor (pdgf: d. waterfield et al. Cancer can be caused by a constitutively expressed growth factor. Alteration of gene expression can contribute to cancer. Growth factors and the like can be drug targets against cancer. A commonly used family of alignment and search tools. Generally considered to be more sensitive than blast. Illustration with two fictitious sequences used in the contig assembly lecture: Cys is the rarest in this protein in the database. If a query sequence contain a c, then go directly to c at site 494 to check; if the query has no c, then report "no match" Motivation: matching short sequences are faster than matching longer ones. Ailv, ilvp, lvpt, vptv, ptvi, tvig, vigc, igct, gctv, ctvp, tvpt. Discard common words (i. e. , words made entirely of common amino acids)
