CUERNAVACA
WINTER SCHOOL OF GENOMICS

GENE PREDICTION
Rodric Guigó i Serra,
Genome Bioinformatics Research Laboratory

CRG-IMIM-UPF

1. Searching for known patterns in DNA Sequences
   1. Consensus sequences, regular expressions
   2. Position specific scoring matrices
   3. Inhomogeneous markov models
   4. PRACTICAL 1 (on your own). Characterization of promoter regions

2. Searching for content in DNA Sequences
   1. Codon bias and the periodic nature of coding DNA
   2. Markov models of coding sequences
   3. PRACTICAL 2 (on your own). Finding coding regions in DNA sequences

3. Gene prediction. The exon chaining solution
   1. The problem.
   2. Scoring of exons.
   3. The "exon chaining" approach for gene prediction (geneid, grail, fgenes,...)
   4. PRACTICAL 3 (on your own). Gene Prediction and reannotation

4. Gene prediction. Hidden Markov Models

5. PRACTICAL 4. Gene Prediction and Annotation of genomic sequences.

6. Sequence similarity based gene prediction (on your own).
   1. EST based gene prediction methods (est2genome, spidey)
   2. Protein based gene prediction methods (genomescan)
   3. Splice Aligment methods (genewise, procrustes)
   4. PRACTICAL 5. Sequence similarity and
      annotation of genomic sequences (UNIX users oriented)
   5. PRACTICAL 5b. Sequence similarity and
      annotation of genomic sequences (Windows users oriented)

7. Comparative gene prediction methods
   1. Overview of the methods
   2. PRACTICAL 6 (on your own). Comparative gene prediction.

8. Gene Prediction in ENCODE

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.

• A Primer on Hidden Markov Models by Robert Castelo
• A Course on GeneFinding