PubMed

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.PMID: 14736341 [PubMed - indexed for MEDLINE]Related articlesFree article

Accurate anchoring alignment of divergent sequences.

Huang W, Umbach DM, Li L.

Bioinformatics. 2006 Jan 1;22(1):29-34. Epub 2005 Nov 13.PMID: 16301203 [PubMed - indexed for MEDLINE]Related articlesFree article

MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution.

Keightley PD, Johnson T.

Genome Res. 2004 Mar;14(3):442-50.PMID: 14993209 [PubMed - indexed for MEDLINE]Related articlesFree article

Detecting the limits of regulatory element conservation and divergence estimation using pairwise and multiple alignments.

Pollard DA, Moses AM, Iyer VN, Eisen MB.

BMC Bioinformatics. 2006 Aug 14;7:376.PMID: 16904011 [PubMed - indexed for MEDLINE]Related articlesFree article

Fast and sensitive multiple alignment of large genomic sequences.

Brudno M, Chapman M, Göttgens B, Batzoglou S, Morgenstern B.

BMC Bioinformatics. 2003 Dec 23;4:66.PMID: 14693042 [PubMed - indexed for MEDLINE]Related articlesFree article

Glocal alignment: finding rearrangements during alignment.

Brudno M, Malde S, Poliakov A, Do CB, Couronne O, Dubchak I, Batzoglou S.

Bioinformatics. 2003;19 Suppl 1:i54-62.PMID: 12855437 [PubMed - indexed for MEDLINE]Related articlesFree article

Analysis of conserved noncoding DNA in Drosophila reveals similar constraints in intergenic and intronic sequences.

Bergman CM, Kreitman M.

Genome Res. 2001 Aug;11(8):1335-45.PMID: 11483574 [PubMed - indexed for MEDLINE]Related articlesFree article

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ.

BMC Bioinformatics. 2003 Oct 10;4:47.PMID: 14552658 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

ReAlignerV: web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences.

Iwama H, Hori Y, Matsumoto K, Murao K, Ishida T.

BMC Bioinformatics. 2008 Feb 22;9:112.PMID: 18294369 [PubMed - indexed for MEDLINE]Related articlesFree article

Noncoding RNA gene detection using comparative sequence analysis.

Rivas E, Eddy SR.

BMC Bioinformatics. 2001;2:8. Epub 2001 Oct 10.PMID: 11801179 [PubMed - indexed for MEDLINE]Related articlesFree article

Purifying selection maintains highly conserved noncoding sequences in Drosophila.

Casillas S, Barbadilla A, Bergman CM.

Mol Biol Evol. 2007 Oct;24(10):2222-34. Epub 2007 Jul 23.PMID: 17646256 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articlesFree article

The regulatory content of intergenic DNA shapes genome architecture.

Nelson CE, Hersh BM, Carroll SB.

Genome Biol. 2004;5(4):R25. Epub 2004 Mar 15.PMID: 15059258 [PubMed - indexed for MEDLINE]Related articlesFree article

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]Related articles

MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution.

Wang J, Keightley PD, Johnson T.

BMC Bioinformatics. 2006 Jun 8;7:292.PMID: 16762073 [PubMed - indexed for MEDLINE]Related articlesFree article

MORPH: probabilistic alignment combined with hidden Markov models of cis-regulatory modules.

Sinha S, He X.

PLoS Comput Biol. 2007 Nov;3(11):e216. Epub 2007 Sep 24.PMID: 17997594 [PubMed - indexed for MEDLINE]Related articlesFree article

Considerations in the identification of functional RNA structural elements in genomic alignments.

Babak T, Blencowe BJ, Hughes TR.

BMC Bioinformatics. 2007 Jan 30;8:33.PMID: 17263882 [PubMed - indexed for MEDLINE]Related articlesFree article

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

Siddharthan R.

BMC Bioinformatics. 2006 Mar 16;7:143.PMID: 16542424 [PubMed - indexed for MEDLINE]Related articlesFree article

How accurately is ncRNA aligned within whole-genome multiple alignments?

Wang AX, Ruzzo WL, Tompa M.

BMC Bioinformatics. 2007 Oct 26;8:417.PMID: 17963514 [PubMed - indexed for MEDLINE]Related articlesFree article