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Items: 1 to 20 of 118

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.

PMID:
23428640
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.

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.

6.

DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment.

Wright ES.

BMC Bioinformatics. 2015 Oct 6;16:322. doi: 10.1186/s12859-015-0749-z.

7.

Accuracy of structure-based sequence alignment of automatic methods.

Kim C, Lee B.

BMC Bioinformatics. 2007 Sep 20;8:355.

8.

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.

9.

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.

PMID:
15941743
10.

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.

11.

Clustal omega.

Sievers F, Higgins DG.

Curr Protoc Bioinformatics. 2014 Dec 12;48:3.13.1-16. doi: 10.1002/0471250953.bi0313s48.

PMID:
25501942
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.

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.

14.
15.

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.

16.

Improved multiple sequence alignments using coupled pattern mining.

Hossain KS, Patnaik D, Laxman S, Jain P, Bailey-Kellogg C, Ramakrishnan N.

IEEE/ACM Trans Comput Biol Bioinform. 2013 Sep-Oct;10(5):1098-112. doi: 10.1109/TCBB.2013.36.

PMID:
24384701
17.

COFFEE: an objective function for multiple sequence alignments.

Notredame C, Holm L, Higgins DG.

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

PMID:
9682054
18.

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.

19.

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
20.

GLProbs: Aligning Multiple Sequences Adaptively.

Ye Y, Cheung DW, Wang Y, Yiu SM, Zhan Q, Lam TW, Ting HF.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jan-Feb;12(1):67-78. doi: 10.1109/TCBB.2014.2316820.

PMID:
26357079

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