INSA: gene prediction, alignment, sequence similarity search

Retrieve a sequence in a database :

Useful links:

 WWW-Query at PBIL
 Entrez at NCBI
 SRS at EBI
 

Exercise 1

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 2

 

Sequence alignments:

Usefuls links:

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)
 

Exercise 3

Gene prediction:

Search and mask repeated sequences