BCB 444/544
Introduction to Bioinformatics

Bioinformatics and Computational Biology
Iowa State University

Required Reading Assignment 1

Altschul SF, Gish W. Local Alignment Statistics Methods Enzymology, 1996; 266:460-80

Prakash A, Tompa M. Statistics of Local Multiple Alignments Bioinformatics, 2005; 21 Suppl 1:i344-50

Reading Assignment 2

Mount Chapter 9 pp 361-385 "Gene Prediction and Regulation"

online: Overview for Chapter 7: "Understanding a Genome Sequence" from Genomes, 2nd Edition, TA Brown

online: Section 7.1: "Locating Genes in a Genome Sequence" from Genomes, 2nd Edition, TA Brown





A. Krogh.
An introduction to hidden Markov models for biological sequences.
In S. L. Salzberg, D. B. Searls, and S. Kasif, editors, Computational Methods in Molecular Biology, chapter 4, pages 45-63. Elsevier, Amsterdam, 1998.

Altschul SF, Madden TL, Schaffer, AA, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997 Sep 1;25(17): 3389-3402.


Required Reading Assignment

Burge, C, Karlin, S. Prediction of Complete Gene Structures in Human Genomic DNA JMB, 1997; 268:78-94.

Optional Reading Assignment

Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., Baker, D. Progress in Modeling of Protein Structures and Interactions Science, 2005; 310:638-642.

Required Reading Assignment

Gibbs, R. Deeper Into the Genome Nature, 2005; 437:1233-1234

Goldstein, D.B., Cavalleri, G.L. Genomics: Understanding Human Diversity Nature, 2005; 437:1241-1242

Optional Reading Assignment

The International HapMap Consortium A Haplotype Map of the Human Genome Nature, 2005; 437:1299-1320