Roderic Guigo, IMIM and UPF, Barcelona

COMPUTATIONAL GENE IDENTIFICATION

Theoretical

1. Introduction
• The Problem. Relevance and difficulty
• Specification of genes in genomic sequences
2. The basic methods
• Search by Signal
• Search by Content
• Database Searches
3. Gene Structure Prediction Programs
• Strategies to integrate heterogenous information
• The Programs
• Accuracy of the Programs
4. Towards Automatic Annotation of Genomic Sequences

Practicals

1. Search Promoter Sequences and Splice Sites

2. Finding Genes in Human Sequences

3. Large Scale Gene Finding. GASP1

Electronic Bibliographies on Computational Gene Identification

• Wential Li
• Misha Gelfand

General Reading

• Fickett J.W., Tung C.-S. (1992), Assessment of protein coding measures, Nucleic Acids Res. 20:6441-6450.
• Milanesi L., Kolchanov N., Rogozin I., Kel A., Titov I. (1994), Sequence functional inference, In "Guide to human genome computing", Bishop M.J., Ed., pp249-312, Academic Press, London.
• Gelfand M.S. (1995), Prediction of function in DNA sequence analysis, J. Comput. Biol. 1:87-115.
• Fickett J.W., Guigó R (1996), Computational gene identification, In "Internet for the Molecular Biologist", Swindell S., Miller R. and Myers G. Eds., pp73-100, Horizon Scientific Press, Wymondham, UK.
• Burset M., Guigó R. (1996), Evaluation of Gene Structure prediction programs, Genomics 34:353-367.
• Fickett J.W. (1996), Finding genes by computer: the state of the art, Trends in Genetics 12 316-320.