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Sequence alignment

BI420 – Introduction to Bioinformatics. Sequence alignment. Gabor T. Marth. Department of Biology, Boston College marth@bc.edu. Sequence alignment – Biology. http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html. Biologically significant sequence alignment. Sequence alignment – Biology.

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Sequence alignment

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

  2. Sequence alignment – Biology http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html Biologically significant sequence alignment

  3. Sequence alignment – Biology http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html Biologically plausible sequence alignment

  4. Sequence alignment – Biology http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html Spurious alignment Examples from: Biological sequence analysis. Durbin, Eddy, Krogh, Mitchison

  5. Alignment types How do we align the words: CRANE and FRAME? CRANE || | FRAME 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 1 + 1 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=-6 S=-10 S=-2 COELACANTH || ||| P-ELICAN-- S=0

  7. Global alignment – Needleman-Wunsch

  8. Local alignment – Smith-Waterman

  9. Visualizing pair-wise alignments http://bioinfo.pbi.nrc.ca:8090/EMBOSS/index.html

  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

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