Lecture: PowerPoint slides

Lecture: PDF slides

Search for sequence similarities in databases :

Useful links:

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

Exercise : BLAST, PSI-BLAST

 

Multiple sequence alignments:

Usefuls links:

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

Exercise : Multiple sequence alignment

Sequence alignment for gene prediction:

Search and mask repeated sequences

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

Prediction of protein-coding genes

1- 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

2- Comparative approach: search protein coding regions by similarity

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

Exercise : sequence alignment for gene prediction

BLAST a sequence database against another one:

Exercise : BLAST all against all