Multiple sequence alignment

Uses

•Pair-wise sequence alignment, Multiple sequence alignment Evolutionary relationships

•Multiple sequence alignment Information structural relationships Information on the most alike regionsPrediction of specific probes

Relationship b/w msa & Evolutionary tree construction

As an extension of sequence pair alignment by

Dynamic programming

Alignment of 3 sequences by DP

Alignment of 3 sequences by DP

Scoring gap penalties by the MSA

Natural gap cost: The sum of the no. of gaps in all pair-wise combinations

Quasi-natural gap cost: Natural cost + additional value for any gap that begins and ends within another

SP model for scoringa msa

Progressive alignment

CLUSTALW

CLUSTALW

CLUSTALW

CLUSTALW