1. Sequence alignment BI420 – Introduction to Bioinformatics
Gabor T. Marth
Department of Biology, Boston College

2. Sequence alignment – Biology
Biologically significant sequence alignment

3. Sequence alignment – Biology
Biologically plausible sequence alignment

4. Sequence alignment – Biology
Spurious alignment
Examples from: Biological sequence analysis. Durbin, Eddy, Krogh, Mitchison

5. Alignment types How do we align the words: CRANE and FRAME? CRANE || |
3 matches, 2 mismatches
How do we align words that are different in length?
COELACANTH
|| |||
P-ELICAN--
COELACANTH
|| |||
-PELICAN--
5 matches, 2 mismatches, 3 gaps
In this case, if we assign +1 points for matches, and -1 for mismatches or gaps, we get 5 x x (-1) + 3 x (-1) = 0. This is the alignment score.
Examples from: BLAST. Korf, Yandell, Bedell

6. Finding the “best” alignment
COELACANTH
| |||
PE-LICAN--
COELACANTH ||
P-EL-ICAN-
COELACANTH
PELICAN--
S=-2
S=-6
S=-10
COELACANTH
|| |||
P-ELICAN--
S=0

7. Global alignment – Needleman-Wunsch-1 -2 -3 -4 -5 -6 -7 -8 -9
-10 P I

8. Local alignment – Smith-WatermanP 1 2 I 3 4

9. Visualizing pair-wise alignments

10. Sequence similarity and scoring
Match-mismatch-gap penalties: e.g. Match = 1 Mismatch = -5 Gap = -10
Scoring matrices

11. Multiple alignments

12. Anchored multiple alignment