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Results: 1 to 20 of 107

1.

Phylo: a citizen science approach for improving multiple sequence alignment.

Kawrykow A, Roumanis G, Kam A, Kwak D, Leung C, Wu C, Zarour E; Phylo players, Sarmenta L, Blanchette M, Waldispühl J.

PLoS One. 2012;7(3):e31362. doi: 10.1371/journal.pone.0031362. Epub 2012 Mar 7.

PMID:
22412834
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment.

Kwak D, Kam A, Becerra D, Zhou Q, Hops A, Zarour E, Kam A, Sarmenta L, Blanchette M, Waldispühl J.

Genome Biol. 2013;14(10):R116.

PMID:
24148814
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences.

Shih AC, Lee DT, Peng CL, Wu YW.

BMC Bioinformatics. 2007 Feb 24;8:63.

PMID:
17319966
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

SLAM web server for comparative gene finding and alignment.

Cawley S, Pachter L, Alexandersson M.

Nucleic Acids Res. 2003 Jul 1;31(13):3507-9.

PMID:
12824355
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

MAVID multiple alignment server.

Bray N, Pachter L.

Nucleic Acids Res. 2003 Jul 1;31(13):3525-6.

PMID:
12824358
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Kalign--an accurate and fast multiple sequence alignment algorithm.

Lassmann T, Sonnhammer EL.

BMC Bioinformatics. 2005 Dec 12;6:298.

PMID:
16343337
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

Shah N, Couronne O, Pennacchio LA, Brudno M, Batzoglou S, Bethel EW, Rubin EM, Hamann B, Dubchak I.

Bioinformatics. 2004 Mar 22;20(5):636-43. Epub 2004 Jan 22.

PMID:
15033870
[PubMed - indexed for MEDLINE]
Free Article
8.

CSA: an efficient algorithm to improve circular DNA multiple alignment.

Fernandes F, Pereira L, Freitas AT.

BMC Bioinformatics. 2009 Jul 23;10:230. doi: 10.1186/1471-2105-10-230.

PMID:
19627599
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

FootPrinter3: phylogenetic footprinting in partially alignable sequences.

Fang F, Blanchette M.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W617-20.

PMID:
16845084
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

PMID:
18366802
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Grammar-based distance in progressive multiple sequence alignment.

Russell DJ, Otu HH, Sayood K.

BMC Bioinformatics. 2008 Jul 10;9:306. doi: 10.1186/1471-2105-9-306.

PMID:
18616828
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

MGAlignIt: A web service for the alignment of mRNA/EST and genomic sequences.

Lee BT, Tan TW, Ranganathan S.

Nucleic Acids Res. 2003 Jul 1;31(13):3533-6.

PMID:
12824360
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Multiple alignment of DNA sequences with MAFFT.

Katoh K, Asimenos G, Toh H.

Methods Mol Biol. 2009;537:39-64. doi: 10.1007/978-1-59745-251-9_3.

PMID:
19378139
[PubMed - indexed for MEDLINE]
14.

MUTAGEN: multi-user tool for annotating genomes.

Brügger K, Redder P, Skovgaard M.

Bioinformatics. 2003 Dec 12;19(18):2480-1.

PMID:
14668237
[PubMed - indexed for MEDLINE]
Free Article
15.

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

Klosterman PS, Uzilov AV, Bendaña YR, Bradley RK, Chao S, Kosiol C, Goldman N, Holmes I.

BMC Bioinformatics. 2006 Oct 3;7:428.

PMID:
17018148
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

ClustalXeed: a GUI-based grid computation version for high performance and terabyte size multiple sequence alignment.

Kim T, Joo H.

BMC Bioinformatics. 2010 Sep 17;11:467. doi: 10.1186/1471-2105-11-467.

PMID:
20849574
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Using multiple alignments to improve seeded local alignment algorithms.

Flannick J, Batzoglou S.

Nucleic Acids Res. 2005 Aug 12;33(14):4563-77. Print 2005.

PMID:
16100379
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

GenomeBlast: a web tool for small genome comparison.

Lu G, Jiang L, Helikar RM, Rowley TW, Zhang L, Chen X, Moriyama EN.

BMC Bioinformatics. 2006 Dec 12;7 Suppl 4:S18.

PMID:
17217510
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
20102627
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.

Brendel V, Xing L, Zhu W.

Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5.

PMID:
14764557
[PubMed - indexed for MEDLINE]
Free Article

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