COLD SPRING HARBOUR
PROGRAMMING FOR BIOLOGY. FALL 2007

GENE PREDICTION
Tyler Alioto and Rodric Guigó i Serra,
Genome Bioinformatics Research Laboratory

Center for Genomic Regulation


  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 4a. Gene Prediction and Annotation of genomic sequences.

  6. PRACTICAL 4b. Gene Prediction and Annotation of genomic sequences. **

  7. 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)

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

  9. 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