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Results: 1 to 20 of 155

1.

DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection.

Chen TW, Wu TH, Ng WV, Lin WC.

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S6. doi: 10.1186/1471-2105-11-S7-S6.

PMID:
21106128
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
24063302
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
11743721
[PubMed - indexed for MEDLINE]
4.

MSOAR: a high-throughput ortholog assignment system based on genome rearrangement.

Fu Z, Chen X, Vacic V, Nan P, Zhong Y, Jiang T.

J Comput Biol. 2007 Nov;14(9):1160-75.

PMID:
17990975
[PubMed - indexed for MEDLINE]
5.

MultiMSOAR 2.0: an accurate tool to identify ortholog groups among multiple genomes.

Shi G, Peng MC, Jiang T.

PLoS One. 2011;6(6):e20892. doi: 10.1371/journal.pone.0020892. Epub 2011 Jun 21.

PMID:
21712981
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Assignment of orthologous genes via genome rearrangement.

Chen X, Zheng J, Fu Z, Nan P, Zhong Y, Lonardi S, Jiang T.

IEEE/ACM Trans Comput Biol Bioinform. 2005 Oct-Dec;2(4):302-15.

PMID:
17044168
[PubMed - indexed for MEDLINE]
7.

Efficient large-scale protein sequence comparison and gene matching to identify orthologs and co-orthologs.

Mahmood K, Webb GI, Song J, Whisstock JC, Konagurthu AS.

Nucleic Acids Res. 2012 Mar;40(6):e44. doi: 10.1093/nar/gkr1261. Epub 2011 Dec 30.

PMID:
22210858
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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]
Free Article
9.

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium.

PLoS Comput Biol. 2012;8(2):e1002386. doi: 10.1371/journal.pcbi.1002386. Epub 2012 Feb 16.

PMID:
22359495
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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]
Free PMC Article
11.

Clustering of main orthologs for multiple genomes.

Fu Z, Jiang T.

J Bioinform Comput Biol. 2008 Jun;6(3):573-84.

PMID:
18574863
[PubMed - indexed for MEDLINE]
12.

Calculating orthologs in bacteria and Archaea: a divide and conquer approach.

Halachev MR, Loman NJ, Pallen MJ.

PLoS One. 2011;6(12):e28388. doi: 10.1371/journal.pone.0028388. Epub 2011 Dec 12.

PMID:
22174796
[PubMed - indexed for MEDLINE]
Free PMC Article
13.
14.

MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

Uchiyama I, Higuchi T, Kawai M.

Nucleic Acids Res. 2010 Jan;38(Database issue):D361-5. doi: 10.1093/nar/gkp948. Epub 2009 Nov 11.

PMID:
19906735
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases.

Wallqvist A, Fukunishi Y, Murphy LR, Fadel A, Levy RM.

Bioinformatics. 2000 Nov;16(11):988-1002.

PMID:
11159310
[PubMed - indexed for MEDLINE]
Free Article
16.

Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).

Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J, Holt I, Liang F, Quackenbush J.

Genome Res. 2002 Mar;12(3):493-502.

PMID:
11875039
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Domain architecture conservation in orthologs.

Forslund K, Pekkari I, Sonnhammer EL.

BMC Bioinformatics. 2011 Aug 5;12:326. doi: 10.1186/1471-2105-12-326.

PMID:
21819573
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Clustering of main orthologs for multiple genomes.

Fu Z, Jiang T.

Comput Syst Bioinformatics Conf. 2007;6:195-201.

PMID:
17951824
[PubMed - indexed for MEDLINE]
Free Article
19.

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.

PMID:
18954438
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.

Mi H, Dong Q, Muruganujan A, Gaudet P, Lewis S, Thomas PD.

Nucleic Acids Res. 2010 Jan;38(Database issue):D204-10. doi: 10.1093/nar/gkp1019. Epub 2009 Dec 16.

PMID:
20015972
[PubMed - indexed for MEDLINE]
Free PMC Article

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