Bioinformatics Module Links

Key Animation Resources

Bioinformatics

• An Introduction to Bioinformatics Algorithms. By Neil C. Jones and Pavel A. Pevzner.
• Bioinformatics: Sequence and Genome Analysis. Second Edition. By David W. Mount.
• Computational Genome Analysis: An Introduction. By Richard C. Deonier, Simon Tavare, and Michale S. Waterman.
• Symposium on Life Science Education. Links to presentations on diverse innovations in bioinformatics education, including this project.

Adobe Flash and ActionScript

• Actionscript.org. Extensive, frequently-updated compilation of tutorials, with active discussion forum.
• Adobe Flash Developer Center. Excellent source of information from the developers of Adobe Flash.
• Flash and Math. Excellent compilation of programming tutorials with an emphasis on mathematical applications.
• Flash Enabled. This site lists tutorials from a variety of sites on the Web and is a good way to find diverse resources.
• Kirupa.com. Many good tutorials for beginners, covering both design and programming in Flash.

Resources for individual Modules

Module 1: Sequence Alignment

Classic papers

• Needleman, Saul B. and Wunsch, Christian D. (1970). A general method applicable to the search for similarities in the amino acid sequence of two proteins. Journal of Molecular Biology 48 (3): 443–53. doi:10.1016/0022-2836(70)90057-4. PMID 5420325.
• Smith, Temple F. and Waterman, Michael S. (1981). Identification of Common Molecular Subsequences. Journal of Molecular Biology 147: 195–197. doi:10.1016/0022-2836(81)90087-5.

Module 2: Database Search

Web pages

• NCBI BLAST web page: BLAST: Basic Local Alignment Search Tool
• NCBI BLAST tutorial

Classic papers

• Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990). Basic local alignment search tool. J Mol Biol 215 (3): 403–410. doi:10.1006/jmbi.1990.9999. PMID 2231712.
• Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, and Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997 Sep 1; 25(17) 3389-402. pmid:9254694.

Module 3: Motif Discovery

Web pages and tools

• The Meme Suite

Reviews and tutorials

• How does DNA sequence motif discovery work? D'haeseleer P. Nat Biotechnol. 2006 Aug;24(8):959-61.
• Stormo GD (2000). DNA binding sites: representation and discovery. Bioinformatics 16 (1): 16–23. doi:10.1093/bioinformatics/16.1.16. PMID 10812473.

Classic papers

• Profile analysis: detection of distantly related proteins. Gribskov M, McLachlan AD, Eisenberg D. Proc Natl Acad Sci U S A. 1987 Jul;84(13):4355-8. Full text
• Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Hertz GZ, Hartzell GW 3rd, Stormo GD. Comput Appl Biosci. 1990 Apr;6(2):81-92.
• Schneider, T.D. & Stephens, R.M. Sequence Logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097–6100

Module 4: Genome Rearrangements

Relevant for our module

• Exact and approximation algorithms for sorting by reversals, with application to genome rearrangement. John Kececioglu and David Sankoff, Algorithmica 13:1/2, 180-210, 1995.
• Genome rearrangements in mammalian evolution: lessons from human and mouse genomes. Pevzner P, Tesler G. Genome Res. 2003 Jan;13(1):37-45.

Classic papers

• Inversions in the Third Chromosome of Wild Races of Drosophila Pseudoobscura, and Their Use in the Study of the History of the Species. Sturtevant AH, Dobzhansky T. Proc Natl Acad Sci U S A. 1936 Jul;22(7):448-50.
• Inversions in the Chromosomes of Drosophila pseudoobscura. Dobzhansky T, Sturtevant AH. Genetics. 1938 Jan;23(1):28-64.
• Edit distance for genome comparison based on non-local operations (D.Sankoff), Combinatorial Pattern Matching. Third Annual Symposium (A. Apostolico, M. Crochemore, Z. Galil, & U. Manber, ed.), Lecture Notes in Computer Science 644. Springer Verlag, p. 121-135
• Lengths of chromosomal segments conserved since divergence of man and mouse. Nadeau JH, Taylor BA. Proc Natl Acad Sci U S A. 1984. Feb;81(3):814-8.

Module 5: Fragment Assembly

Web pages

• About the Human Genome Project

Classic papers

• Roach, JC; Boysen, C; Wang, K; Hood, L (1995). Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics 26: 345–353. doi:10.1016/0888-7543(95)80219-C. PMID 7601461.
• Combinatorial algorithms for DNA sequence assembly. John Kececioglu and Eugene Myers, Algorithmica 13:1/2, 7-51, 1995.
• Human whole-genome shotgun sequencing. Weber JL, Myers EW. Genome Res. 1997 May;7(5):401-9.
• Against a whole-genome shotgun. Green P. Genome Res. 1997 May;7(5):410-7.
• An Eulerian path approach to DNA fragment assembly. Pevzner PA, Tang H, Waterman MS. Proc Natl Acad Sci U S A. 2001 Aug 14;98(17):9748-53.

Module 6: Hidden Markov Models

Classic papers and books

• Richard Durbin, Sean R. Eddy, Anders Krogh, Graeme Mitchison (1999). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press. ISBN 0-521-62971-3.
• Lawrence R. Rabiner (February 1989). A tutorial on Hidden Markov Models and selected applications in speech recognition. Proceedings of the IEEE 77 (2): 257–286. doi:10.1109/5.18626.