BIOL 301 Lecture Notes - Lecture 11: Ubiquitin, Two-Hybrid Screening, Arabidopsis Thaliana
Document Summary
Diff types of info can be gleaned from the web: sequences, structures of proteins and nucleic acids, expression via microarray data, metabolomics, ppi, protein function. Sequence databases: gdna, mrna, cdna, other transcripts. @uniprot formatted as fasta: > name and info, sequenceblahblah. Identity: similarity, homology: total % identical residues total % + extra scoring for conservative substitutions similarity that reflects common evol origin, e(), or e-value, or expected value. = number of matches to the query that"s expected. Basic, but mainstream: use e( )<1e-4, alignments>15a. a, for any blast involving protein, use e( )<1e-10, alignments>100nucls for blastn, @fasta: more exhaustive, complete. Use to refine blast result candidates: e()<0. 01, low complexity sequence: unusual composition bc repetition or bias for specific a. a"s, need to be masked before aligning because they"d create false assumption of evol relationships, @seg, in blast. 2 genes in diff genomes/species are similar: paralogs and orthologs make protein families, check paralog/ortholog via species-specific blasts.
