ArticleNucleic acids research2014
SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Cracking the black box of deep sequence-based protein-protein interaction prediction.Briefings in bioinformatics · 2024Article
- Protein-Coding Gene Families in Prokaryote Genome Comparisons.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Cytoscape stringApp 2.0: Analysis and Visualization of Heterogeneous Biological Networks.Journal of proteome research · 2023Article
- eggNOG 6.0: enabling comparative genomics across 12 535 organisms.Nucleic acids research · 2023Article
- Ten Years of Collaborative Progress in the Quest for Orthologs.Molecular biology and evolution · 2021Article
- eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.Nucleic acids research · 2019Article
- Insecticidal Toxicity ofFrontiers in cellular and infection microbiology · 2018Article
- The 24th annual Nucleic Acids Research database issue: a look back and upcoming changes.Nucleic acids research · 2017Article
- Globally distributed root endophyte Phialocephala subalpina links pathogenic and saprophytic lifestyles.BMC genomics · 2016Article
- SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles.Bioinformatics (Oxford, England) · 2016Article
- eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.Nucleic acids research · 2016Article
- BRENDA in 2015: exciting developments in its 25th year of existence.Nucleic acids research · 2015Article
- Big data and other challenges in the quest for orthologs.Bioinformatics (Oxford, England) · 2014Article
- Genome sequence of Coxiella burnetii strain Namibia.Standards in genomic sciences · 2014Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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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