Tag: HMM

VOGUE 20090520 – Variable Order HMM with Duration

VOGUE 20090520

:: DESCRIPTION

VOGUE is a variable order and gapped HMM with with duration. It uses sequence mining to extract frequent patterns in the data. It then uses these patterns to build a variable order HMM with explicit duration on the gap states, for sequence modeling and classification. VOGUE was applied to model protein sequences, as well as a number of other sequence datasets including weblogs.

::DEVELOPER

Mohammed J. Zaki

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 VOGUE

:: MORE INFORMATION

Citation

Mohammed J. Zaki, Christopher D. Carothers and Boleslaw K. Szymanski,
VOGUE: A Variable Order Hidden Markov Model with Duration based on Frequent Sequence Mining.
ACM Transactions on Knowledge Discovery in Data, 4(1):Article 5. Jan 2010

Sarment 5 – HMM Sequence Partitioning and Maximal Predictive Partitioning

Sarment 5

:: DESCRIPTION

Sarment is a source package of object-oriented Python modules for sequence segmentation via HMM analysis and Maximal Predictive Partitioning.

::DEVELOPER

Laurent Guéguen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Sarment

:: MORE INFORMATION

Citation

Guéguen, L.
Sarment: Python modules for HMM analysis and partitioning of sequences.
Bioinformatics. 2005 Aug 15;21(16):3427-8

RIPSeeker 1.26.0 – de novo RIP Peak Predictions based on HMM.

RIPSeeker 1.26.0

:: DESCRIPTION

RIPSeeker is a free open-source Bioconductor/R package for identifying protein-associated transcripts from RIP-seq experiments.

::DEVELOPER

Yue Li @ The Zhang Lab, University of Toronto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Weindows/Linux/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

 RIPSeeker

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Apr;41(8):e94. doi: 10.1093/nar/gkt142. Epub 2013 Feb 28.
RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.
Li Y1, Zhao DY, Greenblatt JF, Zhang Z.

RefineHMM 1.0.0 – HMM Refinement software

RefineHMM 1.0.0

:: DESCRIPTION

RefineHMM refines an original hidden Markov model (HMM) to find an optimal fit against the evolutionary group that the HMM models, and it does this using through iterative database searches and incremental subsequent adaptation of the seed set.

::DEVELOPER

IFM Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python
  • HMMER

:: DOWNLOAD

 RefineHMM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 27;11:534. doi: 10.1186/1471-2105-11-534.
Subdivision of the MDR superfamily of medium-chain dehydrogenases/reductases through iterative hidden Markov model refinement.
Hedlund J, Jörnvall H, Persson B.

pantherScore 1.03 – PANTHER HMM Scoring tool

pantherScore 1.03

:: DESCRIPTION

 pantherScore scores protein sequences against the entire PANTHER HMM library and analyze your sequences.

::DEVELOPER

Paul D. Thomas

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 pantherScore

:: MORE INFORMATION

parredHMMlib 1.0 – Library for Hardware Accelerated HMM Parallelizing Analysis

parredHMMlib 1.0

:: DESCRIPTION

parredHMMlib is a C++ library implementing the parredForward and parredViterbi algorithms for multi-core CPUs, parallelizing analysis of hidden Markov models with small state spaces.

::DEVELOPER

Andreas Sand.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 parredHMMlib

:: MORE INFORMATION

Citation

Nielsen, J.; Sand, A.;
Algorithms for a Parallel Implementation of Hidden Markov Models with a Small State Space
Parallel and Distributed Processing Workshops and Phd Forum (IPDPSW), 2011 IEEE International Symposium