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Items: 1 to 20 of 217

1.

Computing the P-value of the information content from an alignment of multiple sequences.

Nagarajan N, Jones N, Keich U.

Bioinformatics. 2005 Jun;21 Suppl 1:i311-8. Erratum in: Bioinformatics. 2005 Sep 15;21(18):3700.

PMID:
15961473
2.

Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.

Ng P, Nagarajan N, Jones N, Keich U.

Bioinformatics. 2006 Jul 15;22(14):e393-401.

PMID:
16873498
3.

Fast model-based protein homology detection without alignment.

Hochreiter S, Heusel M, Obermayer K.

Bioinformatics. 2007 Jul 15;23(14):1728-36. Epub 2007 May 8.

PMID:
17488755
4.
5.

Model-based prediction of sequence alignment quality.

Ahola V, Aittokallio T, Vihinen M, Uusipaikka E.

Bioinformatics. 2008 Oct 1;24(19):2165-71. doi: 10.1093/bioinformatics/btn414. Epub 2008 Aug 4.

PMID:
18678587
6.

Finding motifs from all sequences with and without binding sites.

Leung HC, Chin FY.

Bioinformatics. 2006 Sep 15;22(18):2217-23. Epub 2006 Jul 26.

PMID:
16870937
7.

SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.

Zhou H, Zhou Y.

Bioinformatics. 2005 Sep 15;21(18):3615-21. Epub 2005 Jul 14.

PMID:
16020471
8.

MSAProbs: multiple sequence alignment based on pair hidden Markov models and partition function posterior probabilities.

Liu Y, Schmidt B, Maskell DL.

Bioinformatics. 2010 Aug 15;26(16):1958-64. doi: 10.1093/bioinformatics/btq338. Epub 2010 Jun 23.

PMID:
20576627
9.
10.

ARCS: an aggregated related column scoring scheme for aligned sequences.

Song B, Choi JH, Chen G, Szymanski J, Zhang GQ, Tung AK, Kang J, Kim S, Yang J.

Bioinformatics. 2006 Oct 1;22(19):2326-32. Epub 2006 Jul 26.

PMID:
16870930
11.

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
12.

Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment.

Paten B, Herrero J, Beal K, Birney E.

Bioinformatics. 2009 Feb 1;25(3):295-301. doi: 10.1093/bioinformatics/btn630. Epub 2008 Dec 4.

PMID:
19056777
13.

Probalign: multiple sequence alignment using partition function posterior probabilities.

Roshan U, Livesay DR.

Bioinformatics. 2006 Nov 15;22(22):2715-21. Epub 2006 Sep 5.

PMID:
16954142
14.

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
15.

A memory-efficient algorithm for multiple sequence alignment with constraints.

Lu CL, Huang YP.

Bioinformatics. 2005 Jan 1;21(1):20-30. Epub 2004 Sep 16.

PMID:
15374876
16.

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
17.

Probabilistic alignment of motifs with sequences.

Gonnet P, Lisacek F.

Bioinformatics. 2002 Aug;18(8):1091-101.

PMID:
12176832
18.

Pcons5: combining consensus, structural evaluation and fold recognition scores.

Wallner B, Elofsson A.

Bioinformatics. 2005 Dec 1;21(23):4248-54. Epub 2005 Oct 4.

PMID:
16204344
19.

A profile-based deterministic sequential Monte Carlo algorithm for motif discovery.

Liang KC, Wang X, Anastassiou D.

Bioinformatics. 2008 Jan 1;24(1):46-55. Epub 2007 Nov 17.

PMID:
18024972
20.

A case study of high-throughput biological data processing on parallel platforms.

Pekurovsky D, Shindyalov IN, Bourne PE.

Bioinformatics. 2004 Aug 12;20(12):1940-7. Epub 2004 Mar 25.

PMID:
15044237

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