1 / 6

Pairwise profile alignment

Pairwise profile alignment. Usman Roshan BNFO 601. Protein families. PFAM: http://pfam.sanger.ac.uk/ Family alignments can be used to search for new members in a database. Profile-sequence alignment. Given a family alignment, how can we align it to a sequence?

ethan-garner
Download Presentation

Pairwise profile alignment

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Pairwise profile alignment Usman Roshan BNFO 601

  2. Protein families • PFAM: http://pfam.sanger.ac.uk/ • Family alignments can be used to search for new members in a database

  3. Profile-sequence alignment • Given a family alignment, how can we align it to a sequence? • First, we compute a profile of the alignment. • We then align the profile to the sequence using standard dynamic programming. • However, we need to describe how to align a profile vector to a nucleotide or residue.

  4. Profile • A profile can be described by a set of vectors of nucleotide/residue frequencies. • For each position i of the alignment, we we compute the normalized frequency of nucleotides A, C, G, and T

  5. Aligning a profile vector to a nucleotide • ClustalW/MUSCLE • Let f be the profile vector • Score(f,j)= • where S(i,j) is substitution scoring matrix

  6. Aligning a profile vector to a nucleotide • PSI-BLAST • Score(f,i)=log(Qi/Pi) • Pi is the background probability of nucleotide i • qij is a matrix of match/mismatch probabilities • Define gi as • and Qi as

More Related