Taller de Bioinformatica - Clases practicas

16-19 de Octubre 2001, Santiago, Chile

Retrieve a sequence in a database :

Useful links:
WWW-Query at PBIL
Entrez at NCBI
SRS at EBI

Exercise 1
retrieve the sequence of human insulin in the EMBL database. Follow links -> SwissProt -> Prosite, PFAM, note the location of chain A, B and peptide C.

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:

search for homologues of human insulin in the nematode with BLAST or PSI-BLAST

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:

search for homologues of human insulin in vertebrates with BLAST. Align sequences with CLUSTALX. Edit alignment with SEAVIEW. Look at chains A and B.