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Items: 1 to 20 of 354

1.

Protein homology detection by HMM-HMM comparison.

Söding J.

Bioinformatics. 2005 Apr 1;21(7):951-60. Epub 2004 Nov 5. Erratum in: Bioinformatics. 2005 May 1;21(9):2144.

2.

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.

3.

SVM-HUSTLE--an iterative semi-supervised machine learning approach for pairwise protein remote homology detection.

Shah AR, Oehmen CS, Webb-Robertson BJ.

Bioinformatics. 2008 Mar 15;24(6):783-90. doi: 10.1093/bioinformatics/btn028. Epub 2008 Feb 1.

4.
6.

Large-scale comparison of protein sequence alignment algorithms with structure alignments.

Sauder JM, Arthur JW, Dunbrack RL Jr.

Proteins. 2000 Jul 1;40(1):6-22.

PMID:
10813826
7.

Designing patterns for profile HMM search.

Sun Y, Buhler J.

Bioinformatics. 2007 Jan 15;23(2):e36-43.

8.

Visualizing profile-profile alignment: pairwise HMM logos.

Schuster-Böckler B, Bateman A.

Bioinformatics. 2005 Jun 15;21(12):2912-3. Epub 2005 Apr 12.

9.

Hidden Markov model speed heuristic and iterative HMM search procedure.

Johnson LS, Eddy SR, Portugaly E.

BMC Bioinformatics. 2010 Aug 18;11:431. doi: 10.1186/1471-2105-11-431.

10.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

11.
12.

Improving model construction of profile HMMs for remote homology detection through structural alignment.

Bernardes JS, Dávila AM, Costa VS, Zaverucha G.

BMC Bioinformatics. 2007 Nov 9;8:435.

13.

Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure.

Frenkel-Morgenstern M, Voet H, Pietrokovski S.

Bioinformatics. 2005 Jul 1;21(13):2950-6. Epub 2005 May 3.

14.

A comparison of profile hidden Markov model procedures for remote homology detection.

Madera M, Gough J.

Nucleic Acids Res. 2002 Oct 1;30(19):4321-8.

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.

DescFold: a web server for protein fold recognition.

Yan RX, Si JN, Wang C, Zhang Z.

BMC Bioinformatics. 2009 Dec 14;10:416. doi: 10.1186/1471-2105-10-416.

17.

Detection of distant evolutionary relationships between protein families using theory of sequence profile-profile comparison.

Margelevicius M, Venclovas C.

BMC Bioinformatics. 2010 Feb 17;11:89. doi: 10.1186/1471-2105-11-89.

18.

Quasi-consensus-based comparison of profile hidden Markov models for protein sequences.

Kahsay RY, Wang G, Gao G, Liao L, Dunbrack R.

Bioinformatics. 2005 May 15;21(10):2287-93. Epub 2005 Mar 29.

19.
20.

A profile hidden Markov model for signal peptides generated by HMMER.

Zhang Z, Wood WI.

Bioinformatics. 2003 Jan 22;19(2):307-8.

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