A Gene Prediction Based
DNA Sequence Analysis Course
GRIB (IMIM-UPF-CRG)
- Introduction: gene specification and gene structure in eukaryotes
- Searching for known patterns in DNA Sequences
- Consensus sequences, regular expressions
- Position specific scoring matrices
- Inhomogeneous markov models
- PRACTICAL 1. Characterization of promoter regions
- Inferring unknown patterns from functionally related sequences
- Pattern discovery
- Heuristics and iterative algorithms
- Expectation Maximization algorithms
- Searching for content in DNA Sequences
- Codon bias and the periodic nature of coding DNA
- Markov models of coding sequences
- PRACTICAL 2. Finding coding regions in DNA sequences
- Gene prediction
- The problem.
- Scoring of exons.
- The "exon chaining" approach for gene prediction (geneid, grail, fgenes,...)
- Hidden Markov Models for gene prediction (genscan, hmmgene, genie, ...)
- PRACTICAL 3. Gene Prediction and reannotation
- Accuracy of gene prediction methods
- Sequence similarity based gene prediction
- EST based gene prediction methods (est2genome, spidey)
- Protein based gene prediction methods (genomescan)
- Splice Aligment methods (genewise, procrustes)
- PRACTICAL 4. Sequence similarity and
annotation of genomic sequences (UNIX users oriented)
- PRACTICAL 4b. Sequence similarity and
annotation of genomic sequences (Windows users oriented)
- Comparative gene prediction methods
- Overview of the methods
- Pair Hidden Markov Models (slam,...)
- Comparative gene prediction in human and mouse: sgp and twinscan.
- PRACTICAL 5. Comparative gene prediction.
- Gene Annotation of Genomes
- Automatic annotation pipelines and genome browsers
- PRACTICAL 6. Automatic Annotation of genomic sequences.
- The complexity of eukaryotic gene structure
- Promoter regions
- Alternative splicing
- Non-canonical splicing
- Alternative translation
Contributed by
Enrique Blanco
Sergi Castellano
Genis Parra
Roderic Guigo´