BNFO 240

Usman Roshan

Last time

• Traceback for alignment

• How to select the gap penalties?

• Benchmark alignments– Structural superimposition– BAliBASE

Database searching

• Suppose we have a set of 1,000,000 sequences

• You have a query sequence q and want to find the m closest ones in the database---that means 1,000,000 pairwise alignments!

• How to speed up pairwise alignments?

FASTA

• FASTA was the first software for quick searching of a database

• Introduced the idea of searching for k-mers

• Can be done quickly by preprocessing database

FASTA: combine high scoring hits into diagonal runs

BLAST

Key idea: search for k-mers (short matchig substrings) quickly by preprocessing the database.

BLAST

This key idea can also be used for speeding up pairwise alignments when doing multiple sequence alignments

Biologically realistic scoring matrices

• PAM and BLOSUM are most popular• PAM was developed by Margaret

Dayhoff and co-workers in 1978 by examining 1572 mutations between 71 families of closely related proteins

• BLOSUM is more recent and computed from blocks of sequences with sufficient similarity

PAM

• We need to compute the probability transition matrix M which defines the probability of amino acid i converting to j

• Examine a set of closely related sequences which are easy to align---for PAM 1572 mutations between 71 families

• Compute probabilities of change and background probabilities by simple counting

PAM• In this model the unit of evolution is the amount

of evolution that will change 1 in 100 amino acids on the average

The scoring matrix Sab is the ratio of Mab to pb

PAM Mij matrix (x10000)

Multiple sequence alignment

• “Two sequences whisper, multiple sequences shout out loud”---Arthur Lesk

• Computationally very hard---NP-hard

Formally…

Multiple sequence alignment

Unaligned sequences

GGCTT

TAGGCCTT

TAGCCCTTA

ACACTTC

ACTT

Aligned sequences

_G_ _ GCTT_

TAGGCCTT_

TAGCCCTTA

A_ _CACTTC

A_ _C_ CTT_ Conserved regions help us to identify functionality

Sum of pairs score

Sum of pairs score

• What is the sum of pairs score of this alignment?

Profiles

• Before we see how to construct multiple alignments, how do we align two alignments?

• Idea: summarize an alignment using its profile and align the two profiles

Profile alignment

Iterative alignment(heuristic for sum-of-pairs)

• Pick a random sequence from input set S• Do (n-1) pairwise alignments and align to

closest one t in S• Remove t from S and compute profile of

alignment• While sequences remaining in S

– Do |S| pairwise alignments and align to closest one t

– Remove t from S

Iterative alignment

• Once alignment is computed randomly divide it into two parts

• Compute profile of each sub-alignment and realign the profiles

• If sum-of-pairs of the new alignment is better than the previous then keep, otherwise continue with a different division until specified iteration limit

Progressive alignment

• Idea: perform profile alignments in the order dictated by a tree

• Given a guide-tree do a post-order search and align sequences in that order

• Widely used heuristic