The Basic Local Alignment Search Tool (BLAST), developped at NCBI, finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

You can use it online :
  at Pasteur Paris
  at Genoplante-Info
  at Genopole Ouest
  at PRABI
  in Bordeaux
  in Marseille
  at NCBI