http://blast.ncbi.nlm.nih.gov/

BLAST compares a sequence of DNA or amino acids to a massive database and returns information about how similar the sequences are.

The comparison of nucleotide or protein sequences from the same or different organisms is a very powerful tool in molecular biology. By finding similarities between sequences, scientists can infer the function of newly sequenced genes, predict new members of gene families, and explore evolutionary relationships. Now that whole genomes are being sequenced, sequence similarity searching can be used to predict the location and function of protein-coding and transcription-regulation regions in genomic DNA.

http://www.ncbi.nlm.nih.gov/books/NBK21097/