ScanProsite: a reference implementation of a PROSITE scanning tool - PubMed (original) (raw)
Affiliations
- PMID: 15130850
ScanProsite: a reference implementation of a PROSITE scanning tool
Alexandre Gattiker et al. Appl Bioinformatics. 2002.
Abstract
Many different software tools are available publicly to scan the PROSITE database of protein families. However, none of them, to our knowledge, wholly implements the PROSITE syntax, or satisfies all the rules for scanning a pattern against a sequence. We hereby propose a strict definition of how a PROSITE pattern is to be scanned against a sequence, and provide a reference implementation of a tool to scan PROSITE patterns, rules and profiles against protein sequences.
Similar articles
- The PROSITE database.
Hulo N, Bairoch A, Bulliard V, Cerutti L, De Castro E, Langendijk-Genevaux PS, Pagni M, Sigrist CJ. Hulo N, et al. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D227-30. doi: 10.1093/nar/gkj063. Nucleic Acids Res. 2006. PMID: 16381852 Free PMC article. - A distributed computation of Interpro Pfam, PROSITE and ProDom for protein annotation.
Ribeiro Ede O, Zerlotini GG, Lopes IR, Ribeiro VB, Melo AC, Walter ME, Costa MM; BIOFOCO Network. Ribeiro Ede O, et al. Genet Mol Res. 2005 Sep 30;4(3):590-8. Genet Mol Res. 2005. PMID: 16342044 - Fast model-based protein homology detection without alignment.
Hochreiter S, Heusel M, Obermayer K. Hochreiter S, et al. Bioinformatics. 2007 Jul 15;23(14):1728-36. doi: 10.1093/bioinformatics/btm247. Epub 2007 May 8. Bioinformatics. 2007. PMID: 17488755 - Current bioinformatics tools in genomic biomedical research (Review).
Teufel A, Krupp M, Weinmann A, Galle PR. Teufel A, et al. Int J Mol Med. 2006 Jun;17(6):967-73. Int J Mol Med. 2006. PMID: 16685403 Review. - Protein multiple sequence alignment.
Do CB, Katoh K. Do CB, et al. Methods Mol Biol. 2008;484:379-413. doi: 10.1007/978-1-59745-398-1_25. Methods Mol Biol. 2008. PMID: 18592193 Review.
Cited by
- Isolation, genome analysis and tissue localization of Ceratobasidium theobromae, a new encounter pathogen of cassava in Southeast Asia.
Gil-Ordóñez A, Pardo JM, Sheat S, Xaiyavong K, Leiva AM, Arinaitwe W, Winter S, Newby J, Cuellar WJ. Gil-Ordóñez A, et al. Sci Rep. 2024 Aug 5;14(1):18139. doi: 10.1038/s41598-024-69061-8. Sci Rep. 2024. PMID: 39103398 Free PMC article. - Functional characterization and structural prediction of hypothetical proteins in monkeypox virus and identification of potential inhibitors.
Raen R, Islam MM, Islam R, Islam MR, Jarin T. Raen R, et al. Mol Divers. 2024 Jul 24. doi: 10.1007/s11030-024-10935-4. Online ahead of print. Mol Divers. 2024. PMID: 39043911 - An Exploratory Bioinformatic Investigation of Cats' Susceptibility to Coronavirus-Deriving Epitopes.
Buonocore M, De Biase D, Sorrentino D, Giordano A, Paciello O, D'Ursi AM. Buonocore M, et al. Life (Basel). 2024 Mar 2;14(3):334. doi: 10.3390/life14030334. Life (Basel). 2024. PMID: 38541659 Free PMC article. - Intrinsic apoptosis is evolutionarily divergent among metazoans.
Krasovec G, Horkan HR, Quéinnec É, Chambon JP. Krasovec G, et al. Evol Lett. 2023 Nov 16;8(2):267-282. doi: 10.1093/evlett/qrad057. eCollection 2024 Apr. Evol Lett. 2023. PMID: 38525035 Free PMC article. - Genome biology and evolution of mating-type loci in four cereal rust fungi.
Luo Z, McTaggart A, Schwessinger B. Luo Z, et al. PLoS Genet. 2024 Mar 18;20(3):e1011207. doi: 10.1371/journal.pgen.1011207. eCollection 2024 Mar. PLoS Genet. 2024. PMID: 38498573 Free PMC article.
MeSH terms
LinkOut - more resources
Other Literature Sources