Pepmatch is an efficient, deterministic algorithm for scanning a set of peptides against a large database of proteins for sequence identity at or below a specified number of mismatches.

Parameter selection

Pepmatch Parameters

  • Maximum number of mismatches

    • When scanning for hits in the protein database, Pepmatch will return those that have this number of mismatches or less.

  • Proteome

    • The database of proteins to search against. All included proteomes were obtained from Uniprot/Swiss-Prot.

      • Available proteomes include:

        • human

        • mouse

        • cow

        • dog

        • horse

        • pig

        • rabbit

        • rat

  • Include all matches or the best match per peptide

    • Best match per peptide: Returns only one match per query peptide.

    • All matches: Returns all matches at or below the mismatch threshold for the query peptide.


The pepmatch output will look similar to the table below:

Pepmatch Result Table

A row will be returned for every input peptide, regardless of whether a match was found. Peptides that do not match anything in the selected database will have mostly empty fields, except for ‘NA’ in the ‘Mismatches’ fields.

Some of the columns in the table include:

  • Input Sequence

    • Input peptide (query) sequence

  • Matched Sequence

    • Matched peptide sequence from the proteome database.

  • Gene

    • The gene name associated with the peptide hit.

  • Protein ID

    • The Uniprot/Swissprot accession associated with the peptide hit.

  • Protein Name

    • The name of the protein corresponds to the UniProt accession.

  • Mismatches

    • The number of mismatches between the query and matched peptides

  • Mutated Positions

    • Indexes of the positions that differ between the query and matched peptides.

NOTE: Although Pepmatch is an efficient algorithm, the current implementation on the NG Tools site is suboptimal and can take excessive time. This will be addressed in the next release.