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Items: 1 to 20 of 123

1.

StochHMM: a flexible hidden Markov model tool and C++ library.

Lott PC, Korf I.

Bioinformatics. 2014 Jun 1;30(11):1625-6. doi: 10.1093/bioinformatics/btu057. Epub 2014 Jan 30.

2.

MAMOT: hidden Markov modeling tool.

Schütz F, Delorenzi M.

Bioinformatics. 2008 Jun 1;24(11):1399-400. doi: 10.1093/bioinformatics/btn201. Epub 2008 Apr 25.

3.

Algorithms for variable length Markov chain modeling.

Bejerano G.

Bioinformatics. 2004 Mar 22;20(5):788-9. Epub 2004 Jan 29.

4.

HMMCONVERTER 1.0: a toolbox for hidden Markov models.

Lam TY, Meyer IM.

Nucleic Acids Res. 2009 Nov;37(21):e139. doi: 10.1093/nar/gkp662. Epub .

5.

HMMoC--a compiler for hidden Markov models.

Lunter G.

Bioinformatics. 2007 Sep 15;23(18):2485-7. Epub 2007 Jul 10.

6.

HMMEditor: a visual editing tool for profile hidden Markov model.

Dai J, Cheng J.

BMC Genomics. 2008;9 Suppl 1:S8. doi: 10.1186/1471-2164-9-S1-S8.

7.

MRHMMs: multivariate regression hidden Markov models and the variantS.

Lee Y, Ghosh D, Hardison RC, Zhang Y.

Bioinformatics. 2014 Jun 15;30(12):1755-6. doi: 10.1093/bioinformatics/btu070. Epub 2014 Feb 19.

8.

Hidden Markov models for sequence analysis: extension and analysis of the basic method.

Hughey R, Krogh A.

Comput Appl Biosci. 1996 Apr;12(2):95-107.

PMID:
8744772
9.

Efficient representation and P-value computation for high-order Markov motifs.

da Fonseca PG, Guimarães KS, Sagot MF.

Bioinformatics. 2008 Aug 15;24(16):i160-6. doi: 10.1093/bioinformatics/btn282.

10.

Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory.

Churbanov A, Winters-Hilt S.

BMC Bioinformatics. 2008 Apr 30;9:224. doi: 10.1186/1471-2105-9-224.

11.

ToPS: a framework to manipulate probabilistic models of sequence data.

Kashiwabara AY, Bonadio I, Onuchic V, Amado F, Mathias R, Durham AM.

PLoS Comput Biol. 2013;9(10):e1003234. doi: 10.1371/journal.pcbi.1003234. Epub 2013 Oct 3.

12.

Weighting hidden Markov models for maximum discrimination.

Karchin R, Hughey R.

Bioinformatics. 1998;14(9):772-82.

13.

Profile Comparer: a program for scoring and aligning profile hidden Markov models.

Madera M.

Bioinformatics. 2008 Nov 15;24(22):2630-1. doi: 10.1093/bioinformatics/btn504. Epub 2008 Oct 9.

14.
15.

TigrScan and GlimmerHMM: two open source ab initio eukaryotic gene-finders.

Majoros WH, Pertea M, Salzberg SL.

Bioinformatics. 2004 Nov 1;20(16):2878-9. Epub 2004 May 14.

16.

S-SPatt: simple statistics for patterns on Markov chains.

Nuel G.

Bioinformatics. 2005 Jul 1;21(13):3051-2. Epub 2005 Apr 19.

17.

Using hidden Markov models to align multiple sequences.

Mount DW.

Cold Spring Harb Protoc. 2009 Jul;2009(7):pdb.top41. doi: 10.1101/pdb.top41.

PMID:
20147223
18.

Calibrating E-values for hidden Markov models using reverse-sequence null models.

Karplus K, Karchin R, Shackelford G, Hughey R.

Bioinformatics. 2005 Nov 15;21(22):4107-15. Epub 2005 Aug 25.

19.

PHAISTOS: a framework for Markov chain Monte Carlo simulation and inference of protein structure.

Boomsma W, Frellsen J, Harder T, Bottaro S, Johansson KE, Tian P, Stovgaard K, Andreetta C, Olsson S, Valentin JB, Antonov LD, Christensen AS, Borg M, Jensen JH, Lindorff-Larsen K, Ferkinghoff-Borg J, Hamelryck T.

J Comput Chem. 2013 Jul 15;34(19):1697-705. doi: 10.1002/jcc.23292. Epub 2013 Apr 26.

PMID:
23619610
20.

An introduction to hidden Markov models.

Schuster-Böckler B, Bateman A.

Curr Protoc Bioinformatics. 2007 Jun;Appendix 3:Appendix 3A. doi: 10.1002/0471250953.bia03as18. Review.

PMID:
18428778
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