Gene prediction

Search and mask repeated sequences

• RepeatMasker (Genome Center, USA)
• RepeatMasker (Oxford University, UK)

Prediction of protein-coding genes

Review on gene prediction programs

1- Methods ab initio

• Grail (ORNL, USA)
• Genscan (MIT, USA)
• Genscan (DKFZ, Germany)
• Genscan (Pasteur, France)
• GenMark (EBI, UK)
• Splice sites prediction: NetGene2 (CBS, Denmark)
• Translation start site prediction: NetStart (CBS, Denmark)

2- Search for transcribed regions (EST, cDNA) in genomic DNA

• Similarity search (BLASTN/ESTs): BLAST (NCBI, USA)
• Retrieve sequences for NCBI BLAST output: List_NCBI (PBIL, France)
• Assembly of ESTs: CAP3 (PBIL, France)
• Search for ORF: ORF Finder (NCBI, USA)
• cDNA/genomic DNA alignment: SIM4 (PBIL, France)
• cDNA/genomic DNA alignment: GeneSeqer (ISU, USA)

3- Comparative approach: search protein coding regions by similarity

• Search for protein similarities (BLASTX): BLAST (NCBI, USA)
• Search for protein similarities (BLASTX): BLAST (PBIL, France)
• Alignment protein/genomic DNA: Wise2 (Pasteur, France)
• Alignment protein/genomic DNA: Wise2 (Sanger, UK)

Exercise 1

Retrieve a sequence in a database

Useful links

• WWW-Query (PBIL, France)
• Entrez (NCBI, USA)
• SRS (EBI, UK)

Exercise 2

Search for sequence similarities in databases

Useful links

1- Compare one sequence to a sequence database

• BLAST (NCBI, USA)
• BLAST (SIB, Switzerland)
• WU-BLAST and BLAST (EBI, UK)
• BLAST  (PBIL, France)

2- Compare a sequence profile to a sequence database

• PSI-BLAST (NCBI, USA)

3- Compare a sequence to a database of protein motifs

• ProfileScan (SIB, Switzerland)

Exercise 3

Sequence alignments

Usefuls links

Review on web sites and computer tools for sequence alignment

1- Pairwise sequence alignment

• LFASTA (PBIL, France)
• BLAST 2 sequences (NCBI, USA)

2- Multiple alignments

• ClustalW (protein) (PBIL, France)
• ClustalW (DNA) (PBIL, France)
• ClustalW (EBI, UK)
• DIALIGN (BiBiserv, Germany)
• T-Coffee (EMBnet, Switzerland)

Exercise 4

Molecular phylogeny

Usefuls links

Review on phylogeny programs

Phylogenetic programs on line

• Phylip (Pasteur, France)
• BIONJ (Pasteur, France)

Exercise 5