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Items: 1 to 20 of 135

1.

EcoGene-RefSeq: EcoGene tools applied to the RefSeq prokaryotic genomes.

Zhou J, Richardson AJ, Rudd KE.

Bioinformatics. 2013 Aug 1;29(15):1917-8. doi: 10.1093/bioinformatics/btt302. Epub 2013 Jun 4.

2.

EcoGene 3.0.

Zhou J, Rudd KE.

Nucleic Acids Res. 2013 Jan;41(Database issue):D613-24. doi: 10.1093/nar/gks1235. Epub 2012 Nov 28.

3.
4.

Update on RefSeq microbial genomes resources.

Tatusova T, Ciufo S, Federhen S, Fedorov B, McVeigh R, O'Neill K, Tolstoy I, Zaslavsky L.

Nucleic Acids Res. 2015 Jan;43(Database issue):D599-605. doi: 10.1093/nar/gku1062. Epub 2014 Dec 15.

5.

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

Pruitt KD, Tatusova T, Maglott DR.

Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5. Epub 2006 Nov 27.

6.

ProTISA: a comprehensive resource for translation initiation site annotation in prokaryotic genomes.

Hu GQ, Zheng X, Yang YF, Ortet P, She ZS, Zhu H.

Nucleic Acids Res. 2008 Jan;36(Database issue):D114-9. Epub 2007 Oct 16.

7.

The Microbe browser for comparative genomics.

Gattiker A, Dessimoz C, Schneider A, Xenarios I, Pagni M, Rougemont J.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W296-9. doi: 10.1093/nar/gkp268. Epub 2009 Apr 30.

8.

MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.

Cruveiller S, Le Saux J, Vallenet D, Lajus A, Bocs S, Médigue C.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W471-9.

9.

GenColors: accelerated comparative analysis and annotation of prokaryotic genomes at various stages of completeness.

Romualdi A, Siddiqui R, Glöckner G, Lehmann R, Sühnel J.

Bioinformatics. 2005 Sep 15;21(18):3669-71. Epub 2005 Aug 2.

PMID:
16076887
10.

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.

Nucleic Acids Res. 2016 Jan 4;44(D1):D733-45. doi: 10.1093/nar/gkv1189. Epub 2015 Nov 8.

11.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

12.

Comparison of RefSeq protein-coding regions in human and vertebrate genomes.

Fong JH, Murphy TD, Pruitt KD.

BMC Genomics. 2013 Sep 25;14:654. doi: 10.1186/1471-2164-14-654.

13.

The comprehensive microbial resource.

Davidsen T, Beck E, Ganapathy A, Montgomery R, Zafar N, Yang Q, Madupu R, Goetz P, Galinsky K, White O, Sutton G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D340-5. doi: 10.1093/nar/gkp912. Epub 2009 Nov 5.

14.

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide.

Liolios K, Tavernarakis N, Hugenholtz P, Kyrpides NC.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D332-4.

15.

Mouse genome annotation by the RefSeq project.

McGarvey KM, Goldfarb T, Cox E, Farrell CM, Gupta T, Joardar VS, Kodali VK, Murphy MR, O'Leary NA, Pujar S, Rajput B, Rangwala SH, Riddick LD, Webb D, Wright MW, Murphy TD, Pruitt KD.

Mamm Genome. 2015 Oct;26(9-10):379-90. doi: 10.1007/s00335-015-9585-8. Epub 2015 Jul 28.

16.

PGAT: a multistrain analysis resource for microbial genomes.

Brittnacher MJ, Fong C, Hayden HS, Jacobs MA, Radey M, Rohmer L.

Bioinformatics. 2011 Sep 1;27(17):2429-30. doi: 10.1093/bioinformatics/btr418. Epub 2011 Jul 15.

17.
18.

RefSeq microbial genomes database: new representation and annotation strategy.

Tatusova T, Ciufo S, Fedorov B, O'Neill K, Tolstoy I.

Nucleic Acids Res. 2014 Jan;42(Database issue):D553-9. doi: 10.1093/nar/gkt1274. Epub 2013 Dec 6. Erratum in: Nucleic Acids Res. 2015 Apr 20;43(7):3872.

19.

EcoCyc: fusing model organism databases with systems biology.

Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martínez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muñiz-Rascado L, Ong Q, Paley S, Schröder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD.

Nucleic Acids Res. 2013 Jan;41(Database issue):D605-12. doi: 10.1093/nar/gks1027. Epub 2012 Nov 9.

20.

Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes.

Cummings L, Riley L, Black L, Souvorov A, Resenchuk S, Dondoshansky I, Tatusova T.

FEMS Microbiol Lett. 2002 Nov 5;216(2):133-8.

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