ArticleNucleic acids research2010
SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Article
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- iVirus: facilitating new insights in viral ecology with software and community data sets imbedded in a cyberinfrastructure.The ISME journal · 2017Article
- Maximized Autotransporter-Mediated Expression (MATE) for Surface Display and Secretion of Recombinant Proteins inFood technology and biotechnology · 2015Article
- ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling.Nucleic acids research · 2015Article
- Identifying problematic drugs based on the characteristics of their targets.Frontiers in pharmacology · 2015Article
- SeqDepot: streamlined database of biological sequences and precomputed features.Bioinformatics (Oxford, England) · 2014Article
- SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.Nucleic acids research · 2014Article
- The Fusarium graminearum genome reveals more secondary metabolite gene clusters and hints of horizontal gene transfer.PloS one · 2014Article
- eggNOG v4.0: nested orthology inference across 3686 organisms.Nucleic acids research · 2014Article
- Signature protein of the PVC superphylum.Applied and environmental microbiology · 2014Article
- Integrating metagenomic and amplicon databases to resolve the phylogenetic and ecological diversity of the Chlamydiae.The ISME journal · 2014Article
- kClust: fast and sensitive clustering of large protein sequence databases.BMC bioinformatics · 2013Article
- Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl.mBio · 2013Article
- Selected rapporteur summaries from the XX World Congress of Psychiatric Genetics, Hamburg, Germany, October 14-18, 2012.American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2013Article
- Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.Genome biology · 2013Article
- Deciphering the cryptic genome: genome-wide analyses of the rice pathogen Fusarium fujikuroi reveal complex regulation of secondary metabolism and novel metabolites.PLoS pathogens · 2013Article
- Pythoscape: a framework for generation of large protein similarity networks.Bioinformatics (Oxford, England) · 2012Article
- Computational analysis of interactomes: current and future perspectives for bioinformatics approaches to model the host-pathogen interaction space.Methods (San Diego, Calif.) · 2012Review
- Genome comparison of barley and maize smut fungi reveals targeted loss of RNA silencing components and species-specific presence of transposable elements.The Plant cell · 2012Article
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The prediction of protein function as well as the reconstruction of evolutionary genesis employing sequence comparison at large is still the most powerful tool in sequence analysis. Due to the exponential growth of the number of known protein sequences and the subsequent quadratic growth of the similarity matrix, the computation of the Similarity Matrix of Proteins (SIMAP) becomes a computational intensive task. The SIMAP database provides a comprehensive and up-to-date pre-calculation of the protein sequence similarity matrix, sequence-based features and sequence clusters. As of September 2009, SIMAP covers 48 million proteins and more than 23 million non-redundant sequences. Novel features of SIMAP include the expansion of the sequence space by including databases such as ENSEMBL as well as the integration of metagenomes based on their consistent processing and annotation. Furthermore, protein function predictions by Blast2GO are pre-calculated for all sequences in SIMAP and the data access and query functions have been improved. SIMAP assists biologists to query the up-to-date sequence space systematically and facilitates large-scale downstream projects in computational biology. Access to SIMAP is freely provided through the web portal for individuals (http://mips.gsf.de/simap/) and for programmatic access through DAS (http://webclu.bio.wzw.tum.de/das/) and Web-Service (http://mips.gsf.de/webservices/services/SimapService2.0?wsdl).
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