Useful links:

Sequence similarity search

Compare one sequence to a sequence database:

 BLAST at NCBI
 BLAST at EMBnet (Switzerland)
 WU-BLAST  and BLAST  at the EBI (UK)
 BLAST  at PBIL (France)

Compare a sequence motif to a sequence database:

PSI-BLAST at NCBI

Compare a sequence to a  database of protein motifs:

ProfileScan: compare a sequence to a database of protein motifs

Search and mask repeated sequences

• RepeatMasker (USA)
• RepeatMasker (USA)
• RepeatMasker (Heidelberg, Germany)
• Zebrafish RepeatMasker (Sanger Institute, UK)

Prediction of protein-coding genes

 Review on gene prediction programs

1- Methods ab initio

• Grail
• Genscan (Stanford)
• Genscan (Heidelberg)
• Genscan (Paris)
• FGENESH (Sanger Center)
• GenMark (EBI)
•  GeneMark-hmm (eukaryotes)
•  NetGene2: splice sites prediction
•  Translation start site prediction: NetStart

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

• Similarity search(blastn / ESTs): BLAST (NCBI)
• Assembly of ESTs: CAP3
• Search for ORF: ORF Finder (NCBI)
• cDNA/genomic DNA alignment : SIM4
• cDNA/genomic DNA alignment :  GeneSeqer

3- Comparative approach: search protein coding regions by similarity

• Search for protein similarities (blastx): BLAST (NCBI)
• Search for protein similarities (blastx): BLAST (PBIL)
• Alignment protein/genomic DNA: GENEWISE (Pasteur)
• Alignment protein/genomic DNA: GENEWISE (Sanger)

Prediction of RNA genes

• tRNAscan-SE (Wash-U)

Molecular phylogeny

Review on phylogeny programs

Phylogenetic programs on line

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

Sequence alignments:

Review on web sites and computer tools for sequence alignment at PBIL

Pairwise sequence alignment:  LFASTA at PBIL
Pairwise sequence alignment:  BLAST two sequences  at NCBI
Multiple alignment:  Clustalw Protein sequences at PBIL
Multiple alignment:  ClustalW DNA sequences at PBIL
Multiple alignment:   ClustalW at EBI (UK)
Multiple alignment:   DIALIGN at BiBiserv
Multiple alignment:   T-Coffee at EMBnet (Switzerland)