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HMMER web server: 2015 update.

Robert D Finn1, Jody Clements2, William Arndt2

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK HHMI Janelia Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA rdf@ebi.ac.uk.

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Summary
This summary is machine-generated.

The HMMER web server now offers enhanced protein homology search capabilities with improved results visualization and filtering options. New features include taxonomic filtering and expanded protein family databases for more specific and efficient sequence analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • The HMMER web server provides access to protein homology search algorithms.
  • Growth in sequence databases necessitates improved methods for presenting search results.

Purpose of the Study:

  • To describe enhancements to the HMMER web server, including new search algorithms and result presentation methods.
  • To detail the integration of new protein family databases and taxonomic filtering capabilities.

Main Methods:

  • Expansion of search repertoire to include jackhmmer.
  • Development of taxonomic and domain architecture summaries for results presentation.
  • Implementation of a pre-submission taxonomic filter.

Main Results:

  • Enhanced visualization of homology search results through taxonomic and domain architecture summaries.
  • Improved specificity and performance via taxonomic filtering.
  • Expanded protein family libraries including CATH-Gene3D, PIRSF, Superfamily, and TIGRFAMs.

Conclusions:

  • The HMMER web server offers more powerful and user-friendly tools for protein homology searching.
  • Relocation to the European Bioinformatics Institute ensures continued development and accessibility.