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Items: 1 to 20 of 118

1.

Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model.

Jayaraman G, Siddharthan R.

BMC Bioinformatics. 2010 Sep 16;11:464. doi: 10.1186/1471-2105-11-464.

2.

Sigma: multiple alignment of weakly-conserved non-coding DNA sequence.

Siddharthan R.

BMC Bioinformatics. 2006 Mar 16;7:143.

3.

Towards realistic benchmarks for multiple alignments of non-coding sequences.

Kim J, Sinha S.

BMC Bioinformatics. 2010 Jan 26;11:54. doi: 10.1186/1471-2105-11-54.

4.

Benchmarking tools for the alignment of functional noncoding DNA.

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB.

BMC Bioinformatics. 2004 Jan 21;5:6.

5.

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.

Kim J, Ma J.

Nucleic Acids Res. 2011 Aug;39(15):6359-68. doi: 10.1093/nar/gkr334. Epub 2011 May 16.

6.

Dropout alignment allows homology recognition and evolutionary analysis of rDNA intergenic spacers.

Ryu S, Do Y, Fitch DH, Kim W, Mishra B.

J Mol Evol. 2008 Apr;66(4):368-83. doi: 10.1007/s00239-008-9090-8. Epub 2008 Mar 25.

PMID:
18363028
7.

GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.

8.
9.

MAP2: multiple alignment of syntenic genomic sequences.

Ye L, Huang X.

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

10.
11.

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.

Rose D, Hertel J, Reiche K, Stadler PF, Hackerm├╝ller J.

Genomics. 2008 Jul;92(1):65-74. doi: 10.1016/j.ygeno.2008.04.003. Epub 2008 Jun 3.

12.

Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing.

Feng J, Naiman DQ, Cooper B.

Mol Biosyst. 2009 Dec;5(12):1679-87. doi: 10.1039/b903031j. Epub 2009 Apr 30.

PMID:
19452047
13.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

14.

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
16.

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny.

Siddharthan R, Siggia ED, van Nimwegen E.

PLoS Comput Biol. 2005 Dec;1(7):e67. Epub 2005 Dec 9.

17.

Genomic multiple sequence alignments: refinement using a genetic algorithm.

Wang C, Lefkowitz EJ.

BMC Bioinformatics. 2005 Aug 8;6:200.

18.

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
19.

A new protein linear motif benchmark for multiple sequence alignment software.

Perrodou E, Chica C, Poch O, Gibson TJ, Thompson JD.

BMC Bioinformatics. 2008 Apr 25;9:213. doi: 10.1186/1471-2105-9-213.

20.

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