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

By Roland Arnold, Florian Goldenberg, Hans-Werner Mewes, Thomas Rattei. 2013

29 citations recorded by the source corpus.

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.

Subfields: Molecular Biology

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Citations in the corpus

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses (2018, methodology): “OGs were built using best reciprocal hits information derived from an all-against-all Smith-Waterman matrix provided by the SIMAP project (22).”
BRENDA in 2015: exciting developments in its 25th year of existence (2014, methodology): “(iv) The pre-computed BLAST-Matrix SIMAP (SImilarity MAtrix of Proteins) (22) was integrated into our own Basic Local Alignment Search Tool (BLAST) annotation (23).”
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences (2015, methodology): “Protein sequences from the selected organisms and viruses are extracted and used to compute an all-against-all pairwise similarity matrix (Figure 1B), a task that is currently carried out by the SIMAP project (29).”