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Items: 1 to 20 of 55

1.

CASSIOPE: an expert system for conserved regions searches.

Rascol VL, Levasseur A, Chabrol O, Grusea S, Gouret P, Danchin EG, Pontarotti P.

BMC Bioinformatics. 2009 Sep 10;10:284. doi: 10.1186/1471-2105-10-284.

2.

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
3.

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.

4.

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.

5.

Automatic detection of subsystem/pathway variants in genome analysis.

Ye Y, Osterman A, Overbeek R, Godzik A.

Bioinformatics. 2005 Jun;21 Suppl 1:i478-86.

PMID:
15961494
6.

A general pipeline for the development of anchor markers for comparative genomics in plants.

Fredslund J, Madsen LH, Hougaard BK, Nielsen AM, Bertioli D, Sandal N, Stougaard J, Schauser L.

BMC Genomics. 2006 Aug 14;7:207.

7.

GRAST: a new way of genome reduction analysis using comparative genomics.

Toft C, Fares MA.

Bioinformatics. 2006 Jul 1;22(13):1551-61. Epub 2006 Apr 6.

PMID:
16601001
9.

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.

10.

The use of evolutionary biology concepts for genome annotation.

Danchin EG, Levasseur A, Rascol VL, Gouret P, Pontarotti P.

J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):26-36.

PMID:
17016828
11.
12.

Multi-species comparative mapping in silico using the COMPASS strategy.

Liu L, Gong G, Liu Y, Natarajan S, Larkin DM, Everts-van der Wind A, Rebeiz M, Beever JE.

Bioinformatics. 2004 Jan 22;20(2):148-54.

PMID:
14734304
13.

DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes.

SebestyƩn E, Nagy T, Suhai S, Barta E.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S6. doi: 10.1186/1471-2105-10-S6-S6.

14.

Gene context analysis in the Integrated Microbial Genomes (IMG) data management system.

Mavromatis K, Chu K, Ivanova N, Hooper SD, Markowitz VM, Kyrpides NC.

PLoS One. 2009 Nov 24;4(11):e7979. doi: 10.1371/journal.pone.0007979.

15.

Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics.

Haft DH, Selengut JD, Brinkac LM, Zafar N, White O.

Bioinformatics. 2005 Feb 1;21(3):293-306. Epub 2004 Sep 3.

PMID:
15347579
16.

A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.

Pollock DD, Eisen JA, Doggett NA, Cummings MP.

Mol Biol Evol. 2000 Dec;17(12):1776-88. Review.

PMID:
11110893
17.

Gene teams: a new formalization of gene clusters for comparative genomics.

Luc N, Risler JL, Bergeron A, Raffinot M.

Comput Biol Chem. 2003 Feb;27(1):59-67.

PMID:
12798040
18.

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention.

Hufton AL, Mathia S, Braun H, Georgi U, Lehrach H, Vingron M, Poustka AJ, Panopoulou G.

Genome Res. 2009 Nov;19(11):2036-51. doi: 10.1101/gr.093237.109. Epub 2009 Aug 24.

19.

webMGR: an online tool for the multiple genome rearrangement problem.

Lin CH, Zhao H, Lowcay SH, Shahab A, Bourque G.

Bioinformatics. 2010 Feb 1;26(3):408-10. doi: 10.1093/bioinformatics/btp689. Epub 2009 Dec 18.

PMID:
20022974
20.

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