BLAST Database Searching: Understanding BLAST Tools and Techniques for Biology Students, Study notes of Chemistry

Download BLAST Database Searching: Understanding BLAST Tools and Techniques for Biology Students and more Study notes Chemistry in PDF only on Docsity! BLAST Database Searching BME 110: CompBio Tools Todd Lowe April 11, 2006 Admin • Reading: – Claverie, Chapters 7, 8 – NCBI Blast Guide / info page http://www.ncbi.nlm.nih.gov/BLAST/Why.shtml • Homework #1 assigned after this lecture is completed • Class on (all) Thursdays, back in Social Sciences 159 Basic varieties of BLAST blastn nucleotide query nucleotide database blastp protein query protein database blastx nucleotide query* protein database tblastn protein query nucleotide database* tblastx nucleotide query* nucleotide database* *Translated to protein in all six reading frames before comparison (slow & cpu-intensive for databases) How Does it Work? • Searches for short exact matches (word size) • Defaults: – Blastp: 3 amino acids – Blastn: 11 nucleotides • Without a minimum exact match, will MISS real relationships • With “seed hit”, tries to extend alignment in both directions • A fully extended hit is an HSP (high scoring pair) Translated BLAST • DNA-> protein, 3 reading frames upper sequence + 3 reading frames lower sequence • Important when you don’t know or trust gene sequencing quality or annotation • Translating before comparison gives additional sensitivity, avoids reading frame errors due to incorrect gene prediction • Example: Selenocysteine “stop” codon (TGA) Re: The “Twilight Zone” • Less than 25% sequence identity for two protein sequences • May still be homologous, but only similarity of 3-D protein structures can verify similar function Continued on Thursday