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KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters.

Nakaya A, Katayama T, Itoh M, Hiranuka K, Kawashima S, Moriya Y, Okuda S, Tanaka M, Tokimatsu T, Yamanishi Y, Yoshizawa AC, Kanehisa M, Goto S.

Nucleic Acids Res. 2013 Jan;41(Database issue):D353-7. doi: 10.1093/nar/gks1239. Epub 2012 Nov 27.


Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV.

Biol Direct. 2007 Nov 27;2:33.


Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping.

Fujibuchi W, Ogata H, Matsuda H, Kanehisa M.

Nucleic Acids Res. 2000 Oct 15;28(20):4029-36.


The KEGG databases at GenomeNet.

Kanehisa M, Goto S, Kawashima S, Nakaya A.

Nucleic Acids Res. 2002 Jan 1;30(1):42-6.


ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes.

Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I.

Nucleic Acids Res. 2009 Jan;37(Database issue):D448-54. doi: 10.1093/nar/gkn684. Epub 2008 Oct 9.


OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis.

Whiteside MD, Winsor GL, Laird MR, Brinkman FS.

Nucleic Acids Res. 2013 Jan;41(Database issue):D366-76. doi: 10.1093/nar/gks1241. Epub 2012 Nov 29.


Gene annotation and pathway mapping in KEGG.

Aoki-Kinoshita KF, Kanehisa M.

Methods Mol Biol. 2007;396:71-91.


KEGG: Kyoto Encyclopedia of Genes and Genomes.

Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M.

Nucleic Acids Res. 1999 Jan 1;27(1):29-34.


Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

Wolf YI, Makarova KS, Yutin N, Koonin EV.

Biol Direct. 2012 Dec 14;7:46. doi: 10.1186/1745-6150-7-46.


Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.

Remm M, Storm CE, Sonnhammer EL.

J Mol Biol. 2001 Dec 14;314(5):1041-52.


KAAS: an automatic genome annotation and pathway reconstruction server.

Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5. Epub 2007 May 25.


Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.


Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.

Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA.

Genome Res. 2002 Mar;12(3):503-14.


KEGG for linking genomes to life and the environment.

Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y.

Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4. Epub 2007 Dec 12.


Molecular network analysis of diseases and drugs in KEGG.

Kanehisa M.

Methods Mol Biol. 2013;939:263-75. doi: 10.1007/978-1-62703-107-3_17.


MBGD: microbial genome database for comparative analysis.

Uchiyama I.

Nucleic Acids Res. 2003 Jan 1;31(1):58-62.


SyntTax: a web server linking synteny to prokaryotic taxonomy.

Oberto J.

BMC Bioinformatics. 2013 Jan 16;14:4. doi: 10.1186/1471-2105-14-4.


The KEGG resource for deciphering the genome.

Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D277-80.


FUNYBASE: a FUNgal phYlogenomic dataBASE.

Marthey S, Aguileta G, Rodolphe F, Gendrault A, Giraud T, Fournier E, Lopez-Villavicencio M, Gautier A, Lebrun MH, Chiapello H.

BMC Bioinformatics. 2008 Oct 27;9:456. doi: 10.1186/1471-2105-9-456.


Absynte: a web tool to analyze the evolution of orthologous archaeal and bacterial gene clusters.

Despalins A, Marsit S, Oberto J.

Bioinformatics. 2011 Oct 15;27(20):2905-6. doi: 10.1093/bioinformatics/btr473. Epub 2011 Aug 11.

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