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Database Commons - SIMAP

SIMAP

Citations: 7

z-index 0.98

Short name SIMAP
Full name The Similarity Matrix of Proteins
Description The database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage
URL http://liferay.csb.univie.ac.at/portal/web/simap/
Year founded 2008
Last update & version 2015-05-02    v1.0
Availability Free to all users
University/Institution hosted University of Toronto
Address ON M5S 3E1,Canada
City Toronto
Province/State
Country/Region Canada
Contact name Thomas Rattei
Contact email thomas.rattei@univie.ac.at
Data type(s)
Major organism(s)
Keyword(s)
  • protein sequence annotations
  • protein sequence similarities
Publication(s)
  • SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage. [PMID: 24165881]

    Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei
    Nucleic acids research 2014:42(Database issue)
    7 Citations (Google Scholar as of 2016-01-15)

    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.

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Tags

Protein
protein sequence annotations protein sequence similarities

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Xia [2016-03-28]
    • Lin Xia [2015-06-28]
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