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Gene Unprediction with Spurio: A tool to identify spurious protein sequences.
Höps W, Jeffryes M, Bateman A. Höps W, et al. Among authors: bateman a. F1000Res. 2018 Mar 2;7:261. doi: 10.12688/f1000research.14050.1. eCollection 2018. F1000Res. 2018. PMID: 29721311 Free PMC article.
Spurio searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequences. The tblastn matches are used to score the query sequence's likelihood of being a spurious protein prediction using a Gaussi …
Spurio searches the query protein sequence against a prokaryotic nucleotide database using tblastn and identifies homologous sequence …
The HMMER Web Server for Protein Sequence Similarity Search.
Prakash A, Jeffryes M, Bateman A, Finn RD. Prakash A, et al. Among authors: bateman a. Curr Protoc Bioinformatics. 2017 Dec 8;60:3.15.1-3.15.23. doi: 10.1002/cpbi.40. Curr Protoc Bioinformatics. 2017. PMID: 29220076
AntiFam: a tool to help identify spurious ORFs in protein annotation.
Eberhardt RY, Haft DH, Punta M, Martin M, O'Donovan C, Bateman A. Eberhardt RY, et al. Among authors: bateman a. Database (Oxford). 2012 Mar 20;2012:bas003. doi: 10.1093/database/bas003. Print 2012. Database (Oxford). 2012. PMID: 22434837 Free PMC article.
Pfam: the protein families database.
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M. Finn RD, et al. Among authors: bateman a. Nucleic Acids Res. 2014 Jan;42(Database issue):D222-30. doi: 10.1093/nar/gkt1223. Epub 2013 Nov 27. Nucleic Acids Res. 2014. PMID: 24288371 Free PMC article.
The InterPro protein families database: the classification resource after 15 years.
Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD. Mitchell A, et al. Among authors: bateman a. Nucleic Acids Res. 2015 Jan;43(Database issue):D213-21. doi: 10.1093/nar/gku1243. Epub 2014 Nov 26. Nucleic Acids Res. 2015. PMID: 25428371 Free PMC article.
HMMER web server: 2015 update.
Finn RD, Clements J, Arndt W, Miller BL, Wheeler TJ, Schreiber F, Bateman A, Eddy SR. Finn RD, et al. Among authors: bateman a. Nucleic Acids Res. 2015 Jul 1;43(W1):W30-8. doi: 10.1093/nar/gkv397. Epub 2015 May 5. Nucleic Acids Res. 2015. PMID: 25943547 Free PMC article.
942 results