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Items: 1 to 20 of 91

1.

Transposon identification using profile HMMs.

Edlefsen PT, Liu JS.

BMC Genomics. 2010 Feb 10;11 Suppl 1:S10. doi: 10.1186/1471-2164-11-S1-S10.

2.

Transposable element annotation of the rice genome.

Juretic N, Bureau TE, Bruskiewich RM.

Bioinformatics. 2004 Jan 22;20(2):155-60.

4.

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.

5.

Training HMM structure with genetic algorithm for biological sequence analysis.

Won KJ, Prügel-Bennett A, Krogh A.

Bioinformatics. 2004 Dec 12;20(18):3613-9.

6.

Using evolutionary Expectation Maximization to estimate indel rates.

Holmes I.

Bioinformatics. 2005 May 15;21(10):2294-300.

7.

Using guide trees to construct multiple-sequence evolutionary HMMs.

Holmes I.

Bioinformatics. 2003;19 Suppl 1:i147-57.

8.

HMM sampling and applications to gene finding and alternative splicing.

Cawley SL, Pachter L.

Bioinformatics. 2003 Oct;19 Suppl 2:ii36-41.

9.

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

Edgar RC, Sjölander K.

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

10.

Predicting conserved protein motifs with Sub-HMMs.

Horan K, Shelton CR, Girke T.

BMC Bioinformatics. 2010 Apr 26;11:205. doi: 10.1186/1471-2105-11-205.

11.

A clustering approach for estimating parameters of a profile hidden Markov model.

Aghdam R, Pezeshk H, Malekpour SA, Shemehsavar S, Eslahchi C.

Int J Data Min Bioinform. 2013;8(1):66-82.

PMID:
23865165
12.

Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum.

Terrapon N, Gascuel O, Maréchal E, Bréhélin L.

BMC Bioinformatics. 2012 May 1;13:67. doi: 10.1186/1471-2105-13-67.

13.

Extraction of hidden Markov model representations of signal patterns in DNA sequences.

Yada T, Ishikawa M, Tanaka H, Asai K.

Pac Symp Biocomput. 1996:686-96.

14.

A linear memory algorithm for Baum-Welch training.

Miklós I, Meyer IM.

BMC Bioinformatics. 2005 Sep 19;6:231.

15.

Meta-MEME: motif-based hidden Markov models of protein families.

Grundy WN, Bailey TL, Elkan CP, Baker ME.

Comput Appl Biosci. 1997 Aug;13(4):397-406.

PMID:
9283754
16.

Effects of choice of DNA sequence model structure on gene identification accuracy.

Azad RK, Borodovsky M.

Bioinformatics. 2004 May 1;20(7):993-1005.

17.

Hidden Markov models in biology.

Vogl C, Futschik A.

Methods Mol Biol. 2010;609:241-53. doi: 10.1007/978-1-60327-241-4_14.

PMID:
20221923
18.

Comparative ab initio prediction of gene structures using pair HMMs.

Meyer IM, Durbin R.

Bioinformatics. 2002 Oct;18(10):1309-18.

19.

A duplication growth model of gene expression networks.

Bhan A, Galas DJ, Dewey TG.

Bioinformatics. 2002 Nov;18(11):1486-93.

20.

Hidden Markov models incorporating fuzzy measures and integrals for protein sequence identification and alignment.

Bidargaddi NP, Chetty M, Kamruzzaman J.

Genomics Proteomics Bioinformatics. 2008 Jun;6(2):98-110. doi: 10.1016/S1672-0229(08)60025-X.

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