BI420 – Introduction to Bioinformatics. Sequence alignment. Gabor T. Marth. Department of Biology, Boston College email@example.com. Sequence alignment – Biology. http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html. Biologically significant sequence alignment. Sequence alignment – Biology.
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Biologically significant sequence alignment
Biologically plausible sequence alignment
Examples from: Biological sequence analysis. Durbin, Eddy, Krogh, Mitchison
How do we align the words: CRANE and FRAME?
3 matches, 2 mismatches
How do we align words that are different in length?
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 1 + 1 x (-1) + 3 x (-1) = 0. This is the alignment score.
Examples from: BLAST. Korf, Yandell, Bedell
Match-mismatch-gap penalties: e.g. Match = 1 Mismatch = -5 Gap = -10