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    Results: 1 to 20 of 390

    1.

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

    Dai J, Cheng J.

    BMC Genomics. 2008;9 Suppl 1:S8.PMID: 18366621 [PubMed - indexed for MEDLINE]Related articlesFree article

    2.

    A new decoding algorithm for hidden Markov models improves the prediction of the topology of all-beta membrane proteins.

    Fariselli P, Martelli PL, Casadio R.

    BMC Bioinformatics. 2005 Dec 1;6 Suppl 4:S12.PMID: 16351738 [PubMed - indexed for MEDLINE]Related articlesFree article

    3.

    HMM-ModE--improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences.

    Srivastava PK, Desai DK, Nandi S, Lynn AM.

    BMC Bioinformatics. 2007 Mar 27;8:104.PMID: 17389042 [PubMed - indexed for MEDLINE]Related articlesFree article

    4.

    Evaluation of methods for predicting the topology of beta-barrel outer membrane proteins and a consensus prediction method.

    Bagos PG, Liakopoulos TD, Hamodrakas SJ.

    BMC Bioinformatics. 2005 Jan 12;6:7.PMID: 15647112 [PubMed - indexed for MEDLINE]Related articlesFree article

    5.

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

    Churbanov A, Winters-Hilt S.

    BMC Bioinformatics. 2008 Apr 30;9:224.PMID: 18447951 [PubMed - indexed for MEDLINE]Related articlesFree article

    6.

    Analysis of an optimal hidden Markov model for secondary structure prediction.

    Martin J, Gibrat JF, Rodolphe F.

    BMC Struct Biol. 2006 Dec 13;6:25.PMID: 17166267 [PubMed - indexed for MEDLINE]Related articlesFree article

    7.

    Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER.

    Wistrand M, Sonnhammer EL.

    BMC Bioinformatics. 2005 Apr 15;6:99.PMID: 15831105 [PubMed - indexed for MEDLINE]Related articlesFree article

    8.

    HMM Logos for visualization of protein families.

    Schuster-Böckler B, Schultz J, Rahmann S.

    BMC Bioinformatics. 2004 Jan 21;5:7.PMID: 14736340 [PubMed - indexed for MEDLINE]Related articlesFree article

    9.

    Evolutionary models for insertions and deletions in a probabilistic modeling framework.

    Rivas E.

    BMC Bioinformatics. 2005 Mar 21;6:63.PMID: 15780137 [PubMed - indexed for MEDLINE]Related articlesFree article

    10.

    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.PMID: 16123115 [PubMed - indexed for MEDLINE]Related articlesFree article

    11.

    transition priors for protein hidden Markov models: an empirical study towards maximum discrimination.

    Wistrand M, Sonnhammer EL.

    J Comput Biol. 2004;11(1):181-93.PMID: 15072695 [PubMed - indexed for MEDLINE]Related articles

    12.

    Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

    Waack S, Keller O, Asper R, Brodag T, Damm C, Fricke WF, Surovcik K, Meinicke P, Merkl R.

    BMC Bioinformatics. 2006 Mar 16;7:142.PMID: 16542435 [PubMed - indexed for MEDLINE]Related articlesFree article

    13.

    Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.

    Alexandrov V, Gerstein M.

    BMC Bioinformatics. 2004 Jan 9;5:2.PMID: 14715091 [PubMed - indexed for MEDLINE]Related articlesFree article

    14.

    OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif.

    Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM.

    BMC Bioinformatics. 2009 Jul 7;10:208.PMID: 19583839 [PubMed - indexed for MEDLINE]Related articlesFree article

    15.

    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 [PubMed - indexed for MEDLINE]Related articlesFree article

    16.

    Improving profile HMM discrimination by adapting transition probabilities.

    Wistrand M, Sonnhammer EL.

    J Mol Biol. 2004 May 7;338(4):847-54.PMID: 15099750 [PubMed - indexed for MEDLINE]Related articles

    17.

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

    Madera M.

    Bioinformatics. 2008 Nov 15;24(22):2630-1. Epub 2008 Oct 9.PMID: 18845584 [PubMed - indexed for MEDLINE]Related articlesFree article

    18.

    Profile hidden Markov models.

    Eddy SR.

    Bioinformatics. 1998;14(9):755-63. Review.PMID: 9918945 [PubMed - indexed for MEDLINE]Related articlesFree article

    19.

    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.PMID: 9390268 [PubMed - indexed for MEDLINE]Related articlesFree article

    20.

    Sequence alignments and pair hidden Markov models using evolutionary history.

    Knudsen B, Miyamoto MM.

    J Mol Biol. 2003 Oct 17;333(2):453-60.PMID: 14529629 [PubMed - indexed for MEDLINE]Related articles

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