ArticleNucleic acids research2006
SIMAP: the similarity matrix of proteins.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora.PLoS genetics · 2023Article
- Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes.mBio · 2022Article
- Upregulated MUC2 Is an Unfavorable Prognostic Indicator for Rectal Cancer Patients Undergoing Preoperative CCRT.Journal of clinical medicine · 2021Article
- Rare disruptive mutations in ciliary function genes contribute to testicular cancer susceptibility.Nature communications · 2016Article
- Seasonal time bombs: dominant temperate viruses affect Southern Ocean microbial dynamics.The ISME journal · 2016Article
- SANSparallel: interactive homology search against Uniprot.Nucleic acids research · 2015Article
- Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome.The ISME journal · 2015Article
- Modeling ecological drivers in marine viral communities using comparative metagenomics and network analyses.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- An immunity-triggering effector from the Barley smut fungus Ustilago hordei resides in an Ustilaginaceae-specific cluster bearing signs of transposable element-assisted evolution.PLoS pathogens · 2014Article
- SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.Nucleic acids research · 2014Article
- Metabolic reprogramming by viruses in the sunlit and dark ocean.Genome biology · 2013Article
- Evaluation of methods to concentrate and purify ocean virus communities through comparative, replicated metagenomics.Environmental microbiology · 2013Article
- The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology.PloS one · 2013Article
- CORUM: the comprehensive resource of mammalian protein complexes--2009.Nucleic acids research · 2010Article
- SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.Nucleic acids research · 2010Article
- The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs.The EMBO journal · 2009Article
- Relationship between phylogenetic distribution and genomic features in Neurospora crassa.PloS one · 2009Article
- Genome information management and integrated data analysis with HaloLex.Archives of microbiology · 2008Article
- Dissecting colony development of Neurospora crassa using mRNA profiling and comparative genomics approaches.Eukaryotic cell · 2008Article
- ProSAS: a database for analyzing alternative splicing in the context of protein structures.Nucleic acids research · 2008Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Similarity Matrix of Proteins (SIMAP) (http://mips.gsf.de/simap) provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith-Waterman algorithm. Our ProtInfo system allows querying by protein sequences covered by the SIMAP dataset as well as by fragments of these sequences, highly similar sequences and title words. Each sequence in the database is supplemented with pre-calculated features generated by detailed sequence analyses. By providing WWW interfaces as well as web-services, we offer the SIMAP resource as an efficient and comprehensive tool for sequence similarity searches.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.