Searching Sequence databases 1: Searching Sequence databases 1: - PowerPoint PPT Presentation

Searching Sequence databases 1: Searching Sequence databases 1: Blast Blast

Query: Query: >gi|26339572|dbj|BAC33457.1| unnamed protein product [Mus musculus] MSSTKLEDSLSRRNWSSASELNETQEPFLNPTDYDDEEFLRYLWREYLHPKEYEWVLIAGYIIVFVV ALIGNVLVCVAVWKNHHMRTVTNYFIVNLSLADVLVTITCLPATLVVDITETWFFGQSLCKVIPYLQ TVSVSVSVLTLSCIALDRWYAICHPLMFKSTAKRARNSIVVIWIVSCIIMIPQAIVMECSSMLPGLA NKTTLFTVCDEHWGGEVYPKMYHICFFLVTYMAPLCLMILAYLQIFRKLWCRQIPGTSSVVQRKWKQ QQPVSQPRGSGQQSKARISAVAAEIKQIRARRKTARMLMVVLLVFAICYLPISILNVLKRVFGMFTH TEDRETVYAWFTFSHWLVYANSAANPIIYNFLSGKFREEFKAAFSCCLGVHHRQGDRLARGRTSTES RKSLTTQISNFDNVSKLSEHVVLTSISTLPAANGAGPLQNWYLQQGVPSSLLSTWLEV ß ß What is the function of this sequence? What is the function of this sequence? ß ß Is there a human homolog? Is there a human homolog? ß ß Which organelle does it work in? (Secreted/membrane bound) Which organelle does it work in? (Secreted/membrane bound) ß ß Idea: Search a database of known proteins to see if you can find Idea: Search a database of known proteins to see if you can find similar sequences which have a known function similar sequences which have a known function

Querying with Blast Querying with Blast

Blast Results Blast Results • Scores are computed according to a Scores are computed according to a • scoring matrix. matrix. scoring • Identities Identities • • Positives Positives • • E-value E-value • • Gaps Gaps • • Local alignment Local alignment •

Blast HSP Blast HSP

Blast HSP Blast HSP S Id Q beg S beg Q end S end

Computing alignments Computing alignments • What is an alignment? What is an alignment? • • How can we compute How can we compute ‘ ‘good good’ ’ (high scoring) (high scoring) • alignments? alignments?

T G C A A 0 0 -1 -1 -2 -2 -3 -3 -4 -4 -5 -5 -1 -1 1 1 0 0 -1 -1 -2 -2 -3 -3 T -2 -2 0 0 0 0 1 1 0 0 -1 -1 C -3 -3 -1 -1 -1 -1 0 0 2 2 1 1 A -4 -4 -2 -2 -2 -2 -1 -1 1 1 1 1 T