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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:
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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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RNA secondary structure prediction from multiple sequence alignments:
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Sections 10.1-10.3 from Durbin, Eddy, Krogh, and Mitchison's book
and slides 1-28 from
Ruzzo's
CSE 427 lectures
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Jakob Skou Pedersen, Gill Bejerano, Adam Siepel, Kate Rosenbloom,
Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David
Haussler (2006),
"Identification
and Classification of Conserved RNA Secondary Structures in the Human
Genome",
PLoS Computational Biology, vol. 2, no. 4, e33
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Zasha Weinberg and Walter L. Ruzzo (2004),
"Exploiting
conserved structure for faster annotation of non-coding RNAs without
loss of accuracy", Bioinformatics, vol. 20, i334-i341
and slides 29-46 from
Ruzzo's
CSE 427 lectures
- Phylogenetic footprinting to discover DNA regulatory elements:
slides
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