Multiple sequence alignment is used to determine evolutionary relationships and structural relationships between sequences. It provides information on the most similar regions between sequences and can predict specific probes. Multiple sequence alignment extends pairwise sequence alignment through dynamic programming to align three or more sequences simultaneously. Popular multiple sequence alignment programs like CLUSTALW use progressive alignment methods that first align closely related sequences, then progressively align more distantly related sequences.

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