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Lecture 1
Lecture 2
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Basics of molecular biology (conclusion): Sections 2.3-2.8
in the lecture notes of
CSE 527, Winter 2000.
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Global sequence alignment: Sections 3.1-4.1
in the lecture notes of
CSE 527, Winter 2000.
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Web lab: Introduction to BLAST .
Lecture 3
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Local alignment and alignment with affine gap penalty: Sections 4.2-5.4
in the lecture notes of
CSE 527, Winter 2000.
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The algorithm 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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Web lab: Introduction to Clusters of Orthologous Groups
of proteins (COG).
Lecture 4
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BLAST statistics:
Stephen Altschul's primer.
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Amino acid substitution matrices: Sections 6.5.1-6.5.2 of
Ewens, Warren J. and Grant, Gregory R., Statistical Methods in
Bioinformatics : An Introduction, Springer, 2001.
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Global multiple sequence alignment:
Lecture 6 in the lecture notes of
CSE 527, Winter 2000.
Lecture 5
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Comparative genome annotation:
Kamvysselis, M., Patterson, N., Birren, B., Berger, B., and Lander,
E. (2003) "Whole-genome
comparative annotation and regulatory motif discovery in multiple
yeast species". To appear in The Seventh Annual International
Conference on Research in Computational Molecular Biology,
Berlin, April 2003.
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Global multiple sequence alignment by CLUSTAL W:
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Web lab: Introduction to Genome-wide
comparison of Saccharomyces species.
Lecture 6
Lecture 7
Lecture 8
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Statistical significance of weight matrix matches: Tatusov, R.L.,
Altschul, S.F., and Koonin, E.V. (1994) "Detection of conserved
segments in proteins: Iterative scanning of sequence databases with
alignment blocks". Proceedings of the National Academy of Science USA
91:12091-12095.
- Gel electrophoresis.
- Polymerase chain reaction.
Lecture 9
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Sanger sequencing:
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Whole genome shotgun sequencing:
Olken's lecture.
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Repeats that could cause sequence assembly difficulty:
Jurka, J. and Batzer, M. A. (1996)
"Human Repetitive Elements". Encyclopedia of Molecular Biology and
Molecular Medicine, vol. 3, Robert A. Myers (ed.), 240-246.
Lecture 10
Portions of the CSE 590TV Web may be reprinted or adapted for academic
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