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Results: 1 to 20 of 96

1.

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges.

Powell S, Szklarczyk D, Trachana K, Roth A, Kuhn M, Muller J, Arnold R, Rattei T, Letunic I, Doerks T, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2012 Jan;40(Database issue):D284-9. doi: 10.1093/nar/gkr1060. Epub 2011 Nov 16.

PMID:
22096231
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

eggNOG: automated construction and annotation of orthologous groups of genes.

Jensen LJ, Julien P, Kuhn M, von Mering C, Muller J, Doerks T, Bork P.

Nucleic Acids Res. 2008 Jan;36(Database issue):D250-4. Epub 2007 Oct 16.

PMID:
17942413
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations.

Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von Mering C, Doerks T, Jensen LJ, Bork P.

Nucleic Acids Res. 2010 Jan;38(Database issue):D190-5. doi: 10.1093/nar/gkp951. Epub 2009 Nov 9.

PMID:
19900971
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

eggNOG v4.0: nested orthology inference across 3686 organisms.

Powell S, Forslund K, Szklarczyk D, Trachana K, Roth A, Huerta-Cepas J, Gabaldón T, Rattei T, Creevey C, Kuhn M, Jensen LJ, von Mering C, Bork P.

Nucleic Acids Res. 2014 Jan;42(Database issue):D231-9. doi: 10.1093/nar/gkt1253. Epub 2013 Dec 1.

PMID:
24297252
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

OPTIC: orthologous and paralogous transcripts in clades.

Heger A, Ponting CP.

Nucleic Acids Res. 2008 Jan;36(Database issue):D267-70. Epub 2007 Oct 11.

PMID:
17933761
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Phytome: a platform for plant comparative genomics.

Hartmann S, Lu D, Phillips J, Vision TJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D724-30.

PMID:
16381967
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The COG database: an updated version includes eukaryotes.

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

BMC Bioinformatics. 2003 Sep 11;4:41. Epub 2003 Sep 11.

PMID:
12969510
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.

Huerta-Cepas J, Capella-Gutierrez S, Pryszcz LP, Denisov I, Kormes D, Marcet-Houben M, Gabaldón T.

Nucleic Acids Res. 2011 Jan;39(Database issue):D556-60. doi: 10.1093/nar/gkq1109. Epub 2010 Nov 12.

PMID:
21075798
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Orthology prediction methods: a quality assessment using curated protein families.

Trachana K, Larsson TA, Powell S, Chen WH, Doerks T, Muller J, Bork P.

Bioessays. 2011 Oct;33(10):769-80. doi: 10.1002/bies.201100062. Epub 2011 Aug 19.

PMID:
21853451
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

OrthoDB: the hierarchical catalog of eukaryotic orthologs.

Kriventseva EV, Rahman N, Espinosa O, Zdobnov EM.

Nucleic Acids Res. 2008 Jan;36(Database issue):D271-5. Epub 2007 Oct 18.

PMID:
17947323
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

OrthoSelect: a protocol for selecting orthologous groups in phylogenomics.

Schreiber F, Pick K, Erpenbeck D, Wörheide G, Morgenstern B.

BMC Bioinformatics. 2009 Jul 16;10:219. doi: 10.1186/1471-2105-10-219.

PMID:
19607672
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

BLASTO: a tool for searching orthologous groups.

Zhou Y, Landweber LF.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W678-82. Epub 2007 May 5.

PMID:
17483516
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
18042280
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

OrthoSelect: a web server for selecting orthologous gene alignments from EST sequences.

Schreiber F, Wörheide G, Morgenstern B.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W185-8. doi: 10.1093/nar/gkp434. Epub 2009 Jun 2.

PMID:
19491309
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

PHOG: a database of supergenomes built from proteome complements.

Merkeev IV, Novichkov PS, Mironov AA.

BMC Evol Biol. 2006 Jun 22;6:52.

PMID:
16792803
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Inferring hierarchical orthologous groups from orthologous gene pairs.

Altenhoff AM, Gil M, Gonnet GH, Dessimoz C.

PLoS One. 2013;8(1):e53786. doi: 10.1371/journal.pone.0053786. Epub 2013 Jan 14.

PMID:
23342000
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

A phylogenomic gene cluster resource: the Phylogenetically Inferred Groups (PhIGs) database.

Dehal PS, Boore JL.

BMC Bioinformatics. 2006 Apr 11;7:201.

PMID:
16608522
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

INVHOGEN: a database of homologous invertebrate genes.

Paulsen I, von Haeseler A.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D349-53.

PMID:
16381884
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

EDGAR: a software framework for the comparative analysis of prokaryotic genomes.

Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter FJ, Zakrzewski M, Goesmann A.

BMC Bioinformatics. 2009 May 20;10:154. doi: 10.1186/1471-2105-10-154.

PMID:
19457249
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals.

Lee YS, Oh J, Kim YU, Kim N, Yang S, Hwang UW.

Nucleic Acids Res. 2008 Jan;36(Database issue):D938-42. Epub 2007 Oct 16.

PMID:
17940090
[PubMed - indexed for MEDLINE]
Free PMC Article

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