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Items: 1 to 20 of 95


Aligning multiple genomic sequences with the threaded blockset aligner.

Blanchette M, Kent WJ, Riemer C, Elnitski L, Smit AF, Roskin KM, Baertsch R, Rosenbloom K, Clawson H, Green ED, Haussler D, Miller W.

Genome Res. 2004 Apr;14(4):708-15.


MAVID: constrained ancestral alignment of multiple sequences.

Bray N, Pachter L.

Genome Res. 2004 Apr;14(4):693-9.


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.


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

Wang AX, Ruzzo WL, Tompa M.

BMC Bioinformatics. 2007 Oct 26;8:417.


GS-Aligner: a novel tool for aligning genomic sequences using bit-level operations.

Shih AC, Li WH.

Mol Biol Evol. 2003 Aug;20(8):1299-309. Epub 2003 May 30.


Visualization of multiple genome annotations and alignments with the K-BROWSER.

Chakrabarti K, Pachter L.

Genome Res. 2004 Apr;14(4):716-20.


Automated whole-genome multiple alignment of rat, mouse, and human.

Brudno M, Poliakov A, Salamov A, Cooper GM, Sidow A, Rubin EM, Solovyev V, Batzoglou S, Dubchak I.

Genome Res. 2004 Apr;14(4):685-92.


ABC: software for interactive browsing of genomic multiple sequence alignment data.

Cooper GM, Singaravelu SA, Sidow A.

BMC Bioinformatics. 2004 Dec 8;5:192.


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.


GATA: a graphic alignment tool for comparative sequence analysis.

Nix DA, Eisen MB.

BMC Bioinformatics. 2005 Jan 17;6:9.


Multiple whole-genome alignments without a reference organism.

Dubchak I, Poliakov A, Kislyuk A, Brudno M.

Genome Res. 2009 Apr;19(4):682-9. doi: 10.1101/gr.081778.108. Epub 2009 Jan 28.


GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events.

Chu TC, Liu T, Lee DT, Lee GC, Shih AC.

Bioinformatics. 2009 Sep 1;25(17):2188-93. doi: 10.1093/bioinformatics/btp372. Epub 2009 Jun 19.


Evolution of conserved non-coding sequences within the vertebrate Hox clusters through the two-round whole genome duplications revealed by phylogenetic footprinting analysis.

Matsunami M, Sumiyama K, Saitou N.

J Mol Evol. 2010 Dec;71(5-6):427-36. doi: 10.1007/s00239-010-9396-1. Epub 2010 Oct 28.


Fast and sensitive multiple alignment of large genomic sequences.

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

BMC Bioinformatics. 2003 Dec 23;4:66.


Spidey: a tool for mRNA-to-genomic alignments.

Wheelan SJ, Church DM, Ostell JM.

Genome Res. 2001 Nov;11(11):1952-7.


Mind the gaps: evidence of bias in estimates of multiple sequence alignments.

Golubchik T, Wise MJ, Easteal S, Jermiin LS.

Mol Biol Evol. 2007 Nov;24(11):2433-42. Epub 2007 Aug 20.


Genomic multiple sequence alignments: refinement using a genetic algorithm.

Wang C, Lefkowitz EJ.

BMC Bioinformatics. 2005 Aug 8;6:200.

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