Hammock

Hammock is a software tool that can efficiently cluster and align short peptide sequences to identify shared specificity motifs in large datasets. It was designed to process datasets from various sources and can identify clusters of sequences mimicking epitopes of antibody targets, as well as secondary clusters revealing that the antibodies accept some deviations from original epitope sequences. Hammock is available as a standalone program or as a tool for the Galaxy toolboX.

Topic

Small molecules;Protein sites, features and motifs

Detail

  • Operation: Sequence clustering

  • Software interface: Command-line user interface

  • Language: Perl

  • License: GNU General Public License v3

  • Cost: Free

  • Version name: 1.2.0

  • Credit: MEYS-NPS1-LO1413, MH CZ-DRO, GACR.

  • Input: -

  • Output: -

  • Contact: Adam Krejci krejciadam@gmail.com, Petr Muller muller@mou.cz

  • Collection: -

  • Maturity: Stable

Publications

  • Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets.
  • Krejci A, et al. Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. 2016; 32:9-16. doi: 10.1093/bioinformatics/btv522
  • https://doi.org/10.1093/bioinformatics/btv522
  • PMID: 26342231
  • PMC: PMC4681989

Download and documentation

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