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Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs.

Powell BC, Hutchison CA 3rd.

BMC Bioinformatics. 2006 Jan 19;7:31.PMID: 16423288 [PubMed - indexed for MEDLINE]Related articlesFree article

Accurate prediction of orthologous gene groups in microbes.

Wu H, Mao F, Olman V, Xu Y.

Proc IEEE Comput Syst Bioinform Conf. 2005:73-9.PMID: 16447964 [PubMed - indexed for MEDLINE]Related articles

ORFcurator: molecular curation of genes and gene clusters in prokaryotic organisms.

Rosenfeld JA, Sarkar IN, Planet PJ, Figurski DH, DeSalle R.

Bioinformatics. 2004 Dec 12;20(18):3462-5. Epub 2004 Jul 22.PMID: 15271781 [PubMed - indexed for MEDLINE]Related articlesFree article

Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics.

Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Reeve JN, et al.

J Bacteriol. 1997 Nov;179(22):7135-55.PMID: 9371463 [PubMed - indexed for MEDLINE]Related articlesFree article

Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

Wolf YI, Rogozin IB, Kondrashov AS, Koonin EV.

Genome Res. 2001 Mar;11(3):356-72.PMID: 11230160 [PubMed - indexed for MEDLINE]Related articlesFree article

Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs.

Zheng XH, Lu F, Wang ZY, Zhong F, Hoover J, Mural R.

Bioinformatics. 2005 Mar;21(6):703-10. Epub 2004 Sep 30.PMID: 15458983 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 18366802 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.PMID: 16729895 [PubMed - indexed for MEDLINE]Related articlesFree article

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.PMID: 11024184 [PubMed - indexed for MEDLINE]Related articlesFree article

A "polyORFomic" analysis of prokaryote genomes using disabled-homology filtering reveals conserved but undiscovered short ORFs.

Harrison PM, Carriero N, Liu Y, Gerstein M.

J Mol Biol. 2003 Nov 7;333(5):885-92.PMID: 14583187 [PubMed - indexed for MEDLINE]Related articles

Comparative annotation of viral genomes with non-conserved gene structure.

de Groot S, Mailund T, Hein J.

Bioinformatics. 2007 May 1;23(9):1080-9. Epub 2007 Mar 6.PMID: 17341494 [PubMed - indexed for MEDLINE]Related articlesFree article

Multivariate entropy distance method for prokaryotic gene identification.

Ouyang Z, Zhu H, Wang J, She ZS.

J Bioinform Comput Biol. 2004 Jun;2(2):353-73.PMID: 15297987 [PubMed - indexed for MEDLINE]Related articles

GeneSyn: a tool for detecting conserved gene order across genomes.

Pavesi G, Mauri G, Iannelli F, Gissi C, Pesole G.

Bioinformatics. 2004 Jun 12;20(9):1472-4. Epub 2004 Feb 19.PMID: 14976031 [PubMed - indexed for MEDLINE]Related articlesFree article

Improving genome annotations using phylogenetic profile anomaly detection.

Mikkelsen TS, Galagan JE, Mesirov JP.

Bioinformatics. 2005 Feb 15;21(4):464-70. Epub 2004 Sep 16.PMID: 15374867 [PubMed - indexed for MEDLINE]Related articlesFree article

GenoMiner: a tool for genome-wide search of coding and non-coding conserved sequence tags.

Castrignanò T, De Meo PD, Grillo G, Liuni S, Mignone F, Talamo IG, Pesole G.

Bioinformatics. 2006 Feb 15;22(4):497-9. Epub 2005 Nov 2.PMID: 16267081 [PubMed - indexed for MEDLINE]Related articlesFree article

SMASHing regulatory sites in DNA by human-mouse sequence comparisons.

Zavolan M, Socci ND, Rajewsky N, Gaasterlamd T.

Proc IEEE Comput Soc Bioinform Conf. 2003;2:277-86.PMID: 16452803 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article

Re-annotation of genome microbial coding-sequences: finding new genes and inaccurately annotated genes.

Bocs S, Danchin A, Médigue C.

BMC Bioinformatics. 2002;3:5. Epub 2002 Feb 5.PMID: 11879526 [PubMed - indexed for MEDLINE]Related articlesFree article

Reannotation of Shewanella oneidensis genome.

Daraselia N, Dernovoy D, Tian Y, Borodovsky M, Tatusov R, Tatusova T.

OMICS. 2003 Summer;7(2):171-5.PMID: 14506846 [PubMed - indexed for MEDLINE]Related articles

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]Related articlesFree article