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Basics of Molecular Biology
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Pairwise sequence alignment: Lectures 3-5 from CSE
527
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The algorithms behind BLAST:
- Overview of the BLAST Algorithm
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Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman,
D.J. (1990)
"Basic local alignment search tool". Journal of Molecular Biology
215:403-410.
- The first half (on gapped BLAST) of
Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W.,
Lipman D.J. (1997)
"Gapped BLAST and PSI-BLAST: a new generation of protein
database search programs". Nucleic Acids Research, 25:3389-3402.
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BLAST statistics:
Stephen Altschul's primer
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Amino acid substitution matrices: Section 6.5 from Ewens and Grant's book
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Multiple sequence alignment:
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Distance methods for phylogenetic trees: Lecture
4 from Michael
Brudno's lecture notes
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Markov models:
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Motif discovery for predicting regulatory
elements
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Open problems
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