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Results: 1 to 20 of 55

1.

Tools for simulating evolution of aligned genomic regions with integrated parameter estimation.

Varadarajan A, Bradley RK, Holmes IH.

Genome Biol. 2008 Oct 8;9(10):R147. doi: 10.1186/gb-2008-9-10-r147.

PMID:
18840304
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features.

Schlueter SD, Wilkerson MD, Dong Q, Brendel V.

Genome Biol. 2006;7(11):R111.

PMID:
17116260
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Alignment of genomic sequences using DIALIGN.

Morgenstern B.

Methods Mol Biol. 2007;395:195-204.

PMID:
17993675
[PubMed - indexed for MEDLINE]
4.

DNA assembly with gaps (Dawg): simulating sequence evolution.

Cartwright RA.

Bioinformatics. 2005 Nov 1;21 Suppl 3:iii31-8.

PMID:
16306390
[PubMed - indexed for MEDLINE]
Free Article
5.

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.

Bininda-Emonds OR.

BMC Bioinformatics. 2005 Jun 22;6:156.

PMID:
15969769
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Genomics made easier: an introductory tutorial to genome datamining.

Schattner P.

Genomics. 2009 Mar;93(3):187-95. doi: 10.1016/j.ygeno.2008.10.009. Epub 2008 Dec 5.

PMID:
19041391
[PubMed - indexed for MEDLINE]
Free Article
7.

Genomic multiple sequence alignments: refinement using a genetic algorithm.

Wang C, Lefkowitz EJ.

BMC Bioinformatics. 2005 Aug 8;6:200.

PMID:
16086841
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Current bioinformatics tools in genomic biomedical research (Review).

Teufel A, Krupp M, Weinmann A, Galle PR.

Int J Mol Med. 2006 Jun;17(6):967-73. Review.

PMID:
16685403
[PubMed - indexed for MEDLINE]
9.

MAP2: multiple alignment of syntenic genomic sequences.

Ye L, Huang X.

Nucleic Acids Res. 2005 Jan 7;33(1):162-70. Print 2005.

PMID:
15640451
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Genome comparison without alignment using shortest unique substrings.

Haubold B, Pierstorff N, Möller F, Wiehe T.

BMC Bioinformatics. 2005 May 23;6:123.

PMID:
15910684
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Versatile and open software for comparing large genomes.

Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C, Salzberg SL.

Genome Biol. 2004;5(2):R12. Epub 2004 Jan 30.

PMID:
14759262
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The bioinformatics resource for oral pathogens.

Chen T, Abbey K, Deng WJ, Cheng MC.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W734-40.

PMID:
15980574
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

BamView: viewing mapped read alignment data in the context of the reference sequence.

Carver T, Böhme U, Otto TD, Parkhill J, Berriman M.

Bioinformatics. 2010 Mar 1;26(5):676-7. doi: 10.1093/bioinformatics/btq010. Epub 2010 Jan 12.

PMID:
20071372
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Identifying novel constrained elements by exploiting biased substitution patterns.

Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X.

Bioinformatics. 2009 Jun 15;25(12):i54-62. doi: 10.1093/bioinformatics/btp190.

PMID:
19478016
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Brown CT, Xie Y, Davidson EH, Cameron RA.

BMC Bioinformatics. 2005 Mar 24;6:70.

PMID:
15790396
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Comparative genomics tools applied to bioterrorism defence.

Slezak T, Kuczmarski T, Ott L, Torres C, Medeiros D, Smith J, Truitt B, Mulakken N, Lam M, Vitalis E, Zemla A, Zhou CE, Gardner S.

Brief Bioinform. 2003 Jun;4(2):133-49.

PMID:
12846395
[PubMed - indexed for MEDLINE]
Free Article
17.

Discovery of regulatory elements in vertebrates through comparative genomics.

Prakash A, Tompa M.

Nat Biotechnol. 2005 Oct;23(10):1249-56.

PMID:
16211068
[PubMed - indexed for MEDLINE]
18.

The quest for orthologs: finding the corresponding gene across genomes.

Kuzniar A, van Ham RC, Pongor S, Leunissen JA.

Trends Genet. 2008 Nov;24(11):539-51. doi: 10.1016/j.tig.2008.08.009. Epub 2008 Sep 24. Review.

PMID:
18819722
[PubMed - indexed for MEDLINE]
19.

Dcode.org anthology of comparative genomic tools.

Loots GG, Ovcharenko I.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.

PMID:
15980535
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Evolution at the nucleotide level: the problem of multiple whole-genome alignment.

Dewey CN, Pachter L.

Hum Mol Genet. 2006 Apr 15;15 Spec No 1:R51-6. Review.

PMID:
16651369
[PubMed - indexed for MEDLINE]
Free Article

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