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Items: 1 to 20 of 103

1.

The whole alignment and nothing but the alignment: the problem of spurious alignment flanks.

Frith MC, Park Y, Sheetlin SL, Spouge JL.

Nucleic Acids Res. 2008 Oct;36(18):5863-71. doi: 10.1093/nar/gkn579. Epub 2008 Sep 16.

2.

Parameters for accurate genome alignment.

Frith MC, Hamada M, Horton P.

BMC Bioinformatics. 2010 Feb 9;11:80. doi: 10.1186/1471-2105-11-80.

3.

Evolution at the nucleotide level: the problem of multiple whole-genome alignment.

Dewey CN, Pachter L.

Hum Mol Genet. 2006 Apr 15;15 Spec No 1:R51-6. Review.

PMID:
16651369
4.

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities.

Roshan U, Chikkagoudar S, Livesay DR.

BMC Bioinformatics. 2008 Jan 28;9:61. doi: 10.1186/1471-2105-9-61.

5.
6.

Separating significant matches from spurious matches in DNA sequences.

Devillers H, Schbath S.

J Comput Biol. 2012 Jan;19(1):1-12. doi: 10.1089/cmb.2011.0070. Epub 2011 Dec 9.

7.

PSAR: measuring multiple sequence alignment reliability by probabilistic sampling.

Kim J, Ma J.

Nucleic Acids Res. 2011 Aug;39(15):6359-68. doi: 10.1093/nar/gkr334. Epub 2011 May 16.

8.

Uncertainty in homology inferences: assessing and improving genomic sequence alignment.

Lunter G, Rocco A, Mimouni N, Heger A, Caldeira A, Hein J.

Genome Res. 2008 Feb;18(2):298-309. Epub 2007 Dec 11.

9.

SFESA: a web server for pairwise alignment refinement by secondary structure shifts.

Tong J, Pei J, Grishin NV.

BMC Bioinformatics. 2015 Sep 3;16:282. doi: 10.1186/s12859-015-0711-0.

10.

Significance of gapped sequence alignments.

Newberg LA.

J Comput Biol. 2008 Nov;15(9):1187-94. doi: 10.1089/cmb.2008.0125.

11.

Towards a reliable objective function for multiple sequence alignments.

Thompson JD, Plewniak F, Ripp R, Thierry JC, Poch O.

J Mol Biol. 2001 Dec 7;314(4):937-51.

PMID:
11734009
12.

On the significance of sequence alignments when using multiple scoring matrices.

Frommlet F, Futschik A, Bogdan M.

Bioinformatics. 2004 Apr 12;20(6):881-7. Epub 2004 Jan 29.

PMID:
14751984
13.

Sigma-2: Multiple sequence alignment of non-coding DNA via an evolutionary model.

Jayaraman G, Siddharthan R.

BMC Bioinformatics. 2010 Sep 16;11:464. doi: 10.1186/1471-2105-11-464.

14.

DIALIGN-T: an improved algorithm for segment-based multiple sequence alignment.

Subramanian AR, Weyer-Menkhoff J, Kaufmann M, Morgenstern B.

BMC Bioinformatics. 2005 Mar 22;6:66.

15.

Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments.

Sierk ML, Smoot ME, Bass EJ, Pearson WR.

BMC Bioinformatics. 2010 Mar 22;11:146. doi: 10.1186/1471-2105-11-146.

16.

Ancestral sequence alignment under optimal conditions.

Hudek AK, Brown DG.

BMC Bioinformatics. 2005 Nov 17;6:273.

17.

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.

18.

Structure alignment based on coding of local geometric measures.

Chang PL, Rinne AW, Dewey TG.

BMC Bioinformatics. 2006 Jul 14;7:346.

19.
20.

PhyLAT: a phylogenetic local alignment tool.

Sun H, Buhler JD.

Bioinformatics. 2012 May 15;28(10):1336-44. doi: 10.1093/bioinformatics/bts158. Epub 2012 Apr 6.

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