COLD SPRING HARBOUR
PROGRAMMING FOR BIOLOGY. FALL 2007
Center for Genomic Regulation
- Searching for known patterns in DNA Sequences **
- Consensus sequences, regular expressions
- Position specific scoring matrices
- Inhomogeneous markov models
- PRACTICAL 1 (on your own). Characterization of promoter regions
- Searching for content in DNA Sequences **
- Codon bias and the periodic nature of coding DNA
- Markov models of coding sequences
- PRACTICAL 2 (on your own). Finding coding regions in DNA sequences
- Gene prediction. The exon chaining solution **
- The problem.
- Scoring of exons.
- The "exon chaining" approach for gene prediction (geneid, grail, fgenes,...)
- PRACTICAL 3 (on your own). Gene Prediction and reannotation
- Gene prediction. Hidden Markov Models
- PRACTICAL 4a. Gene Prediction and Annotation of genomic sequences.
- PRACTICAL 4b. Gene Prediction and Annotation of genomic sequences. **
- Sequence similarity based gene prediction (on your own).
- EST based gene prediction methods (est2genome, spidey)
- Protein based gene prediction methods (genomescan)
- Splice Aligment methods (genewise, procrustes)
- PRACTICAL 5. Sequence similarity and annotation of genomic sequences (UNIX users oriented) **
- PRACTICAL 5b. Sequence similarity and
annotation of genomic sequences (Windows users oriented)
- Comparative gene prediction methods
- Overview of the methods
- PRACTICAL 6 (on your own). Comparative gene prediction.
- Gene Prediction in ENCODE
REFERENCES
Brent and Guigó (2004), Recent advances in gene structure prediction,
Current Opinion in Structural Biology 14:264-272
[pdf]
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. R. Durbin, S. Eddy, A. Krogh and G. Mitchinson. Cambridge University Press, 1998.
EGASP'05: ENCODE Genome Annotation Assessment Project
OTHER LINKS
Contributions by
Enrique Blanco
Sergi Castellano
Genis Parra
Josep F. Abril