BPS 4104 Study Guide - Final Guide: Dna Replication, Sequence Logo, Stop Codon
27 Mar 2018
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Why string matching: 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, m. d. waterfield et al. Nature 304:35-39: r. f. doolittle et al. Implications: 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. Fasta: 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: Exact match: all sequences in the database are pre-indexed, 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.
