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Items 1 - 20 of 131
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1:

Multi-species sequence comparison: the next frontier in genome annotation.

Dubchak I, Frazer K.

Genome Biol. 2003;4(12):122. Epub 2003 Nov 27.

PMID: 14659006 [PubMed - indexed for MEDLINE]

2:

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.

PMID: 15590941 [PubMed - indexed for MEDLINE]

3:

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]

4:

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]

5:

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.

PMID: 15655071 [PubMed - indexed for MEDLINE]

6:

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]

7:

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.

Bergman CM, Pfeiffer BD, Rincón-Limas DE, Hoskins RA, Gnirke A, Mungall CJ, Wang AM, Kronmiller B, Pacleb J, Park S, Stapleton M, Wan K, George RA, de Jong PJ, Botas J, Rubin GM, Celniker SE.

Genome Biol. 2002;3(12):RESEARCH0086. Epub 2002 Dec 30.

PMID: 12537575 [PubMed - indexed for MEDLINE]

8:

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation.

Cvijović M, Dalevi D, Bilsland E, Kemp GJ, Sunnerhagen P.

BMC Bioinformatics. 2007 Aug 8;8:295.

PMID: 17686169 [PubMed - indexed for MEDLINE]

9:

Discovering and detecting transposable elements in genome sequences.

Bergman CM, Quesneville H.

Brief Bioinform. 2007 Nov;8(6):382-92. Epub 2007 Oct 10. Review.

PMID: 17932080 [PubMed - indexed for MEDLINE]

10:

Evidence for turnover of functional noncoding DNA in mammalian genome evolution.

Smith NG, Brandström M, Ellegren H.

Genomics. 2004 Nov;84(5):806-13.

PMID: 15475259 [PubMed - indexed for MEDLINE]

11:

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons.

Wang QF, Prabhakar S, Chanan S, Cheng JF, Rubin EM, Boffelli D.

Genome Biol. 2007;8(1):R1.

PMID: 17201929 [PubMed - indexed for MEDLINE]

12:

PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences.

Elnitski L, Riemer C, Petrykowska H, Florea L, Schwartz S, Miller W, Hardison R.

Genomics. 2002 Dec;80(6):681-90.

PMID: 12504859 [PubMed - indexed for MEDLINE]

13:

Using PhyloCon to identify conserved regulatory motifs.

Wang T.

Curr Protoc Bioinformatics. 2007 Sep;Chapter 2:Unit 2.12.

PMID: 18428790 [PubMed - indexed for MEDLINE]

14:

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences.

Hughes JR, Cheng JF, Ventress N, Prabhakar S, Clark K, Anguita E, De Gobbi M, de Jong P, Rubin E, Higgs DR.

Proc Natl Acad Sci U S A. 2005 Jul 12;102(28):9830-5. Epub 2005 Jul 5.

PMID: 15998734 [PubMed - indexed for MEDLINE]

16:

LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.

Brudno M, Do CB, Cooper GM, Kim MF, Davydov E; NISC Comparative Sequencing Program, Green ED, Sidow A, Batzoglou S.

Genome Res. 2003 Apr;13(4):721-31. Epub 2003 Mar 12.

PMID: 12654723 [PubMed - indexed for MEDLINE]

17:

EnteriX 2003: Visualization tools for genome alignments of Enterobacteriaceae.

Florea L, McClelland M, Riemer C, Schwartz S, Miller W.

Nucleic Acids Res. 2003 Jul 1;31(13):3527-32.

PMID: 12824359 [PubMed - indexed for MEDLINE]

18:

Computation and analysis of genomic multi-sequence alignments.

Blanchette M.

Annu Rev Genomics Hum Genet. 2007;8:193-213. Review.

PMID: 17489682 [PubMed - indexed for MEDLINE]

19:

Tree Gibbs Sampler: identifying conserved motifs without aligning orthologous sequences.

Cai X, Hu H, Li XS.

Bioinformatics. 2007 Aug 1;23(15):2013-4. Epub 2007 May 31.

PMID: 17540681 [PubMed - indexed for MEDLINE]

20:

Combining phylogenetic data with co-regulated genes to identify regulatory motifs.

Wang T, Stormo GD.

Bioinformatics. 2003 Dec 12;19(18):2369-80.

PMID: 14668220 [PubMed - indexed for MEDLINE]

Items 1 - 20 of 131
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