Multiple sequence alignment

1. Multiple sequence
alignment

2. Uses
•Pair-wise sequence alignment, Multiple sequence
alignment Evolutionary relationships
•Multiple sequence alignment
Information structural relationships
Information on the most alike regions
Prediction of specific probes

3. Relationship b/w msa &
Evolutionary tree construction

4. As an extension of
sequence pair alignment by
Dynamic programming

5. Alignment of 3 sequences by
DP

6. Alignment of 3 sequences by
DP

7. 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

8. SP model for scoring
a msa

9. Progressive alignment

12. CLUSTALW

13. CLUSTALW

14. CLUSTALW

15. CLUSTALW