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Items: 1 to 20 of 72

1.

A novel hybrid gene prediction method employing protein multiple sequence alignments.

Keller O, Kollmar M, Stanke M, Waack S.

Bioinformatics. 2011 Mar 15;27(6):757-63. doi: 10.1093/bioinformatics/btr010. Epub 2011 Jan 6.

PMID:
21216780
2.
3.

Analysis and prediction of functional sub-types from protein sequence alignments.

Hannenhalli SS, Russell RB.

J Mol Biol. 2000 Oct 13;303(1):61-76.

PMID:
11021970
5.

COACH: profile-profile alignment of protein families using hidden Markov models.

Edgar RC, Sjölander K.

Bioinformatics. 2004 May 22;20(8):1309-18. Epub 2004 Feb 12.

PMID:
14962937
6.

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
8.

Multiple sequence alignment.

Edgar RC, Batzoglou S.

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

PMID:
16679011
9.

WASABI: an automated sequence processing system for multigene phylogenies.

Kauff F, Cox CJ, Lutzoni F.

Syst Biol. 2007 Jun;56(3):523-31. No abstract available.

PMID:
17562476
10.

JIGSAW: integration of multiple sources of evidence for gene prediction.

Allen JE, Salzberg SL.

Bioinformatics. 2005 Sep 15;21(18):3596-603. Epub 2005 Aug 2.

PMID:
16076884
11.

SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.

Melvin I, Ie E, Kuang R, Weston J, Stafford WN, Leslie C.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S2.

12.

PROMALS: towards accurate multiple sequence alignments of distantly related proteins.

Pei J, Grishin NV.

Bioinformatics. 2007 Apr 1;23(7):802-8. Epub 2007 Jan 31.

PMID:
17267437
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.

A computational pipeline for protein structure prediction and analysis at genome scale.

Shah M, Passovets S, Kim D, Ellrott K, Wang L, Vokler I, LoCascio P, Xu D, Xu Y.

Bioinformatics. 2003 Oct 12;19(15):1985-96.

PMID:
14555633
15.

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
16.

An improved general amino acid replacement matrix.

Le SQ, Gascuel O.

Mol Biol Evol. 2008 Jul;25(7):1307-20. doi: 10.1093/molbev/msn067. Epub 2008 Mar 26.

PMID:
18367465
17.

PFRES: protein fold classification by using evolutionary information and predicted secondary structure.

Chen K, Kurgan L.

Bioinformatics. 2007 Nov 1;23(21):2843-50. Epub 2007 Oct 17.

PMID:
17942446
18.

Aligning multiple protein sequences by parallel hybrid genetic algorithm.

Nguyen HD, Yoshihara I, Yamamori K, Yasunaga M.

Genome Inform. 2002;13:123-32.

PMID:
14571381
19.
20.

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

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