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Items: 1 to 20 of 137

1.

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.

Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75.

2.

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.

PMID:
8743695
3.

Making automated multiple alignments of very large numbers of protein sequences.

Sievers F, Dineen D, Wilm A, Higgins DG.

Bioinformatics. 2013 Apr 15;29(8):989-95. doi: 10.1093/bioinformatics/btt093. Epub 2013 Feb 21.

4.

Simple chained guide trees give high-quality protein multiple sequence alignments.

Boyce K, Sievers F, Higgins DG.

Proc Natl Acad Sci U S A. 2014 Jul 22;111(29):10556-61. doi: 10.1073/pnas.1405628111. Epub 2014 Jul 7.

5.

A new progressive-iterative algorithm for multiple structure alignment.

Lupyan D, Leo-Macias A, Ortiz AR.

Bioinformatics. 2005 Aug 1;21(15):3255-63. Epub 2005 Jun 7.

6.

High quality protein sequence alignment by combining structural profile prediction and profile alignment using SABER-TOOTH.

Teichert F, Minning J, Bastolla U, Porto M.

BMC Bioinformatics. 2010 May 14;11:251. doi: 10.1186/1471-2105-11-251.

7.

OD-seq: outlier detection in multiple sequence alignments.

Jehl P, Sievers F, Higgins DG.

BMC Bioinformatics. 2015 Aug 25;16:269. doi: 10.1186/s12859-015-0702-1.

8.

Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.

Lin HN, Notredame C, Chang JM, Sung TY, Hsu WL.

PLoS One. 2011;6(12):e27872. doi: 10.1371/journal.pone.0027872. Epub 2011 Dec 2.

9.

PROMALS web server for accurate multiple protein sequence alignments.

Pei J, Kim BH, Tang M, Grishin NV.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W649-52. Epub 2007 Apr 22.

10.

COFFEE: an objective function for multiple sequence alignments.

Notredame C, Holm L, Higgins DG.

Bioinformatics. 1998 Jun;14(5):407-22.

11.

vALId: validation of protein sequence quality based on multiple alignment data.

Bianchetti L, Thompson JD, Lecompte O, Plewniak F, Poch O.

J Bioinform Comput Biol. 2005 Aug;3(4):929-47.

PMID:
16078368
12.

Progressive multiple alignment using sequence triplet optimizations and three-residue exchange costs.

Konagurthu AS, Whisstock J, Stuckey PJ.

J Bioinform Comput Biol. 2004 Dec;2(4):719-45.

PMID:
15617163
13.
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15.

Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs.

Sadreyev RI, Grishin NV.

Bioinformatics. 2004 Apr 12;20(6):818-28. Epub 2004 Jan 29.

16.

Formatt: Correcting protein multiple structural alignments by incorporating sequence alignment.

Daniels NM, Nadimpalli S, Cowen LJ.

BMC Bioinformatics. 2012 Oct 6;13:259. doi: 10.1186/1471-2105-13-259.

17.

Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix.

Ndhlovu A, Hazelhurst S, Durand PM.

BMC Bioinformatics. 2015 Aug 14;16:255. doi: 10.1186/s12859-015-0688-8.

18.

Multiple sequence alignment with user-defined constraints at GOBICS.

Morgenstern B, Werner N, Prohaska SJ, Steinkamp R, Schneider I, Subramanian AR, Stadler PF, Weyer-Menkhoff J.

Bioinformatics. 2005 Apr 1;21(7):1271-3. Epub 2004 Nov 16.

19.

Iterative non-sequential protein structural alignment.

Salem S, Zaki MJ.

Comput Syst Bioinformatics Conf. 2008;7:183-94.

20.

Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment.

Ferragina P, Giancarlo R, Greco V, Manzini G, Valiente G.

BMC Bioinformatics. 2007 Jul 13;8:252.

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