Pfam is a domain-based protein database.

A query against the protein database is then run using this profile, and a larger group of proteins is found.

UniProt Consortium also provides a Metalink for their large protein database.

To determine which epitopes are shared between pathogen and self, large protein databases are used.

We have placed around 15,000 known genes in the genome, and described 33,000 that have substantial homology to the major protein databases.

Those tags are then used to match, accounting amino acid mutations, the sequences in a protein database.

The peptide masses are compared to protein databases such as Swissprot, which contain protein sequence information.

This program, given a protein query, returns the most similar protein sequences from the protein database that the user specifies.

A peptide sequence tag obtained by tandem mass spectrometry can be used to identify a peptide in a protein database.

When researchers looked in protein databases, trying to match viral protein fragments with self-protein fragments, their amino acids did not always line up exactly.