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A roadmap for the functional annotation of protein families: a community perspective.
de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O'Donoghue S, Orengo C, O'Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J. de Crécy-Lagard V, et al. Database (Oxford). 2022 Aug 12;2022:baac062. doi: 10.1093/database/baac062. Database (Oxford). 2022. PMID: 35961013 Free PMC article.
Plant genome annotation methods.
Ouyang S, Thibaud-Nissen F, Childs KL, Zhu W, Buell CR. Ouyang S, et al. Methods Mol Biol. 2009;513:263-82. doi: 10.1007/978-1-59745-427-8_14. Methods Mol Biol. 2009. PMID: 19347655
RefSeq: an update on mammalian reference sequences.
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, Farrell CM, Hart J, Landrum MJ, McGarvey KM, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Shkeda A, Sun H, Tamez P, Tully RE, Wallin C, Webb D, Weber J, Wu W, DiCuccio M, Kitts P, Maglott DR, Murphy TD, Ostell JM. Pruitt KD, et al. Nucleic Acids Res. 2014 Jan;42(Database issue):D756-63. doi: 10.1093/nar/gkt1114. Epub 2013 Nov 19. Nucleic Acids Res. 2014. PMID: 24259432 Free PMC article.
Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.
O'Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, Rajput B, Robbertse B, Smith-White B, Ako-Adjei D, Astashyn A, Badretdin A, Bao Y, Blinkova O, Brover V, Chetvernin V, Choi J, Cox E, Ermolaeva O, Farrell CM, Goldfarb T, Gupta T, Haft D, Hatcher E, Hlavina W, Joardar VS, Kodali VK, Li W, Maglott D, Masterson P, McGarvey KM, Murphy MR, O'Neill K, Pujar S, Rangwala SH, Rausch D, Riddick LD, Schoch C, Shkeda A, Storz SS, Sun H, Thibaud-Nissen F, Tolstoy I, Tully RE, Vatsan AR, Wallin C, Webb D, Wu W, Landrum MJ, Kimchi A, Tatusova T, DiCuccio M, Kitts P, Murphy TD, Pruitt KD. O'Leary NA, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. doi: 10.1093/nar/gkv1189. Epub 2015 Nov 8. Nucleic Acids Res. 2016. PMID: 26553804 Free PMC article.
RefSeq: an update on prokaryotic genome annotation and curation.
Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR, Gwadz M, Lu F, Marchler GH, Song JS, Thanki N, Yamashita RA, Zheng C, Thibaud-Nissen F, Geer LY, Marchler-Bauer A, Pruitt KD. Haft DH, et al. Nucleic Acids Res. 2018 Jan 4;46(D1):D851-D860. doi: 10.1093/nar/gkx1068. Nucleic Acids Res. 2018. PMID: 29112715 Free PMC article.
Database resources of the National Center for Biotechnology Information.
Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC, Funk K, Ketter A, Kim S, Kimchi A, Kitts PA, Kuznetsov A, Lathrop S, Lu Z, McGarvey K, Madden TL, Murphy TD, O'Leary N, Phan L, Schneider VA, Thibaud-Nissen F, Trawick BW, Pruitt KD, Ostell J. Sayers EW, et al. Nucleic Acids Res. 2020 Jan 8;48(D1):D9-D16. doi: 10.1093/nar/gkz899. Nucleic Acids Res. 2020. PMID: 31602479 Free PMC article.
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation.
Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS, Gonzales NR, Gwadz M, Lanczycki CJ, Song JS, Thanki N, Wang J, Yamashita RA, Yang M, Zheng C, Marchler-Bauer A, Thibaud-Nissen F. Li W, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1020-D1028. doi: 10.1093/nar/gkaa1105. Nucleic Acids Res. 2021. PMID: 33270901 Free PMC article.
Assembly: a resource for assembled genomes at NCBI.
Kitts PA, Church DM, Thibaud-Nissen F, Choi J, Hem V, Sapojnikov V, Smith RG, Tatusova T, Xiang C, Zherikov A, DiCuccio M, Murphy TD, Pruitt KD, Kimchi A. Kitts PA, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D73-80. doi: 10.1093/nar/gkv1226. Epub 2015 Nov 17. Nucleic Acids Res. 2016. PMID: 26578580 Free PMC article.
Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly.
Schneider VA, Graves-Lindsay T, Howe K, Bouk N, Chen HC, Kitts PA, Murphy TD, Pruitt KD, Thibaud-Nissen F, Albracht D, Fulton RS, Kremitzki M, Magrini V, Markovic C, McGrath S, Steinberg KM, Auger K, Chow W, Collins J, Harden G, Hubbard T, Pelan S, Simpson JT, Threadgold G, Torrance J, Wood JM, Clarke L, Koren S, Boitano M, Peluso P, Li H, Chin CS, Phillippy AM, Durbin R, Wilson RK, Flicek P, Eichler EE, Church DM. Schneider VA, et al. Genome Res. 2017 May;27(5):849-864. doi: 10.1101/gr.213611.116. Epub 2017 Apr 10. Genome Res. 2017. PMID: 28396521 Free PMC article.
Towards complete and error-free genome assemblies of all vertebrate species.
Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW 3rd, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnso… See abstract for full author list ➔ Rhie A, et al. Nature. 2021 Apr;592(7856):737-746. doi: 10.1038/s41586-021-03451-0. Epub 2021 Apr 28. Nature. 2021. PMID: 33911273 Free PMC article.
61 results