SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage

Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)
81 Downloads (Pure)

Abstract

The Similarity Matrix of Proteins (SIMAP, http://mips.gsf.de/simap/) database has been designed to massively accelerate computationally expensive protein sequence analysis tasks in bioinformatics. It provides pre-calculated sequence similarities interconnecting the entire known protein sequence universe, complemented by pre-calculated protein features and domains, similarity clusters and functional annotations. SIMAP covers all major public protein databases as well as many consistently re-annotated metagenomes from different repositories. As of September 2013, SIMAP contains >163 million proteins corresponding to ∼70 million non-redundant sequences. SIMAP uses the sensitive FASTA search heuristics, the Smith-Waterman alignment algorithm, the InterPro database of protein domain models and the BLAST2GO functional annotation algorithm. SIMAP assists biologists by facilitating the interactive exploration of the protein sequence universe. Web-Service and DAS interfaces allow connecting SIMAP with any other bioinformatic tool and resource. All-against-all protein sequence similarity matrices of project-specific protein collections are generated on request. Recent improvements allow SIMAP to cover the rapidly growing sequenced protein sequence universe. New Web-Service interfaces enhance the connectivity of SIMAP. Novel tools for interactive extraction of protein similarity networks have been added. Open access to SIMAP is provided through the web portal; the portal also contains instructions and links for software access and flat file downloads.

Original languageEnglish
Pages (from-to)D279-D284
Number of pages6
JournalNucleic Acids Research
Volume42
Issue numberD1
Early online date26 Oct 2013
DOIs
Publication statusPublished - Jan 2014

Keywords

  • Databases, Protein
  • Internet
  • Molecular Sequence Annotation
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Sequence Analysis, Protein
  • User-Computer Interface
  • Journal Article
  • Research Support, Non-U.S. Gov't

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