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Results: 1 to 20 of 88

1.

Finding functional sequence elements by multiple local alignment.

Frith MC, Hansen U, Spouge JL, Weng Z.

Nucleic Acids Res. 2004 Jan 2;32(1):189-200. Print 2004.

PMID:
14704356
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
16477324
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

A local multiple alignment method for detection of non-coding RNA sequences.

Tabei Y, Asai K.

Bioinformatics. 2009 Jun 15;25(12):1498-505. doi: 10.1093/bioinformatics/btp261. Epub 2009 Apr 17.

PMID:
19376823
[PubMed - indexed for MEDLINE]
Free Article
4.

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.

PMID:
15590941
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

T-Coffee: A novel method for fast and accurate multiple sequence alignment.

Notredame C, Higgins DG, Heringa J.

J Mol Biol. 2000 Sep 8;302(1):205-17.

PMID:
10964570
[PubMed - indexed for MEDLINE]
6.

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]
Free Article
7.

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome.

Matveeva OV, Foley BT, Nemtsov VA, Gesteland RF, Matsufuji S, Atkins JF, Ogurtsov AY, Shabalina SA.

BMC Bioinformatics. 2004 Apr 29;5:44.

PMID:
15115544
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles.

Gautheret D, Lambert A.

J Mol Biol. 2001 Nov 9;313(5):1003-11.

PMID:
11700055
[PubMed - indexed for MEDLINE]
9.

New techniques for DNA sequence classification.

Wang JT, Rozen S, Shapiro BA, Shasha D, Wang Z, Yin M.

J Comput Biol. 1999 Summer;6(2):209-18.

PMID:
10421523
[PubMed - indexed for MEDLINE]
10.

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]
Free PMC Article
11.

Discovering sequence motifs with arbitrary insertions and deletions.

Frith MC, Saunders NF, Kobe B, Bailey TL.

PLoS Comput Biol. 2008 May 9;4(4):e1000071. doi: 10.1371/journal.pcbi.1000071.

PMID:
18437229
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

A simulated annealing algorithm for finding consensus sequences.

Keith JM, Adams P, Bryant D, Kroese DP, Mitchelson KR, Cochran DA, Lala GH.

Bioinformatics. 2002 Nov;18(11):1494-9.

PMID:
12424121
[PubMed - indexed for MEDLINE]
Free Article
13.

Rapid detection of conserved regions in protein sequences using wavelets.

Krishnan A, Li KB, Issac P.

In Silico Biol. 2004;4(2):133-48.

PMID:
15107019
[PubMed - indexed for MEDLINE]
14.

Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals.

Vanet A, Marsan L, Labigne A, Sagot MF.

J Mol Biol. 2000 Mar 24;297(2):335-53.

PMID:
10715205
[PubMed - indexed for MEDLINE]
15.

Localized motif discovery in gene regulatory sequences.

Narang V, Mittal A, Sung WK.

Bioinformatics. 2010 May 1;26(9):1152-9. doi: 10.1093/bioinformatics/btq106. Epub 2010 Mar 11.

PMID:
20223835
[PubMed - indexed for MEDLINE]
Free Article
16.

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
17.

Dynamic use of multiple parameter sets in sequence alignment.

Huang X, Brutlag DL.

Nucleic Acids Res. 2007;35(2):678-86. Epub 2006 Dec 19.

PMID:
17182633
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

AL2CO: calculation of positional conservation in a protein sequence alignment.

Pei J, Grishin NV.

Bioinformatics. 2001 Aug;17(8):700-12.

PMID:
11524371
[PubMed - indexed for MEDLINE]
Free Article
19.

STAMP: a web tool for exploring DNA-binding motif similarities.

Mahony S, Benos PV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W253-8. Epub 2007 May 3.

PMID:
17478497
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
14693042
[PubMed - indexed for MEDLINE]
Free PMC Article

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