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Items: 1 to 20 of 107

1.

Quality measures for protein alignment benchmarks.

Edgar RC.

Nucleic Acids Res. 2010 Apr;38(7):2145-53. doi: 10.1093/nar/gkp1196. Epub 2010 Jan 4.

2.

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark.

Thompson JD, Koehl P, Ripp R, Poch O.

Proteins. 2005 Oct 1;61(1):127-36.

3.

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.

4.

DNA reference alignment benchmarks based on tertiary structure of encoded proteins.

Carroll H, Beckstead W, O'Connor T, Ebbert M, Clement M, Snell Q, McClellan D.

Bioinformatics. 2007 Oct 1;23(19):2648-9. Epub 2007 Aug 8.

PMID:
17686799
5.
6.
7.

APDB: a novel measure for benchmarking sequence alignment methods without reference alignments.

O'Sullivan O, Zehnder M, Higgins D, Bucher P, Grosdidier A, Notredame C.

Bioinformatics. 2003;19 Suppl 1:i215-21.

PMID:
12855461
8.

Matt: local flexibility aids protein multiple structure alignment.

Menke M, Berger B, Cowen L.

PLoS Comput Biol. 2008 Jan;4(1):e10. doi: 10.1371/journal.pcbi.0040010.

9.

MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information.

Pei J, Grishin NV.

Nucleic Acids Res. 2006;34(16):4364-74. Epub 2006 Aug 26. Erratum in: Nucleic Acids Res. 2006;34(20):6064.

10.

ProbCons: Probabilistic consistency-based multiple sequence alignment.

Do CB, Mahabhashyam MS, Brudno M, Batzoglou S.

Genome Res. 2005 Feb;15(2):330-40.

11.

Multiple sequence alignment.

Edgar RC, Batzoglou S.

Curr Opin Struct Biol. 2006 Jun;16(3):368-73. Epub 2006 May 5. Review.

PMID:
16679011
12.

Benchmarking tools for the alignment of functional noncoding DNA.

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB.

BMC Bioinformatics. 2004 Jan 21;5:6.

13.

SABmark--a benchmark for sequence alignment that covers the entire known fold space.

Van Walle I, Lasters I, Wyns L.

Bioinformatics. 2005 Apr 1;21(7):1267-8. Epub 2004 Aug 27.

PMID:
15333456
14.

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
15.

Multiple sequence alignment based on profile alignment of intermediate sequences.

Lu Y, Sze SH.

J Comput Biol. 2008 Sep;15(7):767-77. doi: 10.1089/cmb.2007.0132.

PMID:
18662101
16.

MUSCLE: multiple sequence alignment with high accuracy and high throughput.

Edgar RC.

Nucleic Acids Res. 2004 Mar 19;32(5):1792-7. Print 2004.

17.

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.

18.

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.

19.

[Verification of the PREFAB alignment database].

Astakhova TV, Lobanov MN, Poverennaia IV, RoÄ­tberg MA, Iakovlev VV.

Biofizika. 2012 Mar-Apr;57(2):205-11. Russian.

PMID:
22594274
20.

MSAIndelFR: a scheme for multiple protein sequence alignment using information on indel flanking regions.

Al-Shatnawi M, Ahmad MO, Swamy MN.

BMC Bioinformatics. 2015 Nov 23;16:393. doi: 10.1186/s12859-015-0826-3.

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