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 scoring matrix. matrix.

• Identities

Identities

• Positives

Positives

• E-value

E-value

• Gaps

Gaps

• Local alignment

Local alignment

Blast HSP Blast HSP

Blast HSP Blast HSP

Q beg S beg Q end S end S Id

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?

1 1 1 1

• 1
• 1
• 2
• 2
• 2
• 2
• 4
• 4

1 1 2 2

• 1
• 1
• 1
• 1
• 3
• 3
• 1
• 1

1 1

• 2
• 2
• 3
• 3
• 2
• 2
• 1
• 1

1 1

• 1
• 1
• 5
• 5
• 4
• 4
• 3
• 3
• 2
• 2
• 1
• 1

T G C A A T C A T