Tag: Hidden Markov Model

NHMMFDR 1.0.6 – non-homogeneous Hidden Markov Model based FDR control

NHMMFDR 1.0.6

:: DESCRIPTION

NHMMFDR is an R package that implements the non-homogeneous Hidden Markov Model based FDR control for multiple comparison adjustment under dependence.

::DEVELOPER

Pei Fen Kuan

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 NHMMFDR

:: MORE INFORMATION

Citation

Kuan, P., and Chiang, D.Y., (2012).
Integrating Prior Knowledge in Multiple Testing Under Dependence with Applications in Detecting Differential DNA Methylation.
Biometrics,DOI: 10.1111/j.1541-0420.2011.01730.x

FISH 0.2 – Fast Genotype Imputation with Segmental Hidden Markov model.

FISH 0.2

:: DESCRIPTION

FISH is a java program for fast and accurate diploid genotype imputation.

::DEVELOPER

Dr. Lei Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 FISH

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 31. [Epub ahead of print]
FISH: fast and accurate diploid genotype imputation via segmental hidden Markov model.
Zhang L1, Pei YF, Fu X, Lin Y, Wang YP, Deng HW.

GHMM 0.9 – General Hidden Markov Model library

GHMM 0.9

:: DESCRIPTION

The GHMM is a freely available C library implementing efficient data structures and algorithms for basic and extended HMMs with discrete and continous emissions.

::DEVELOPER

Schliep lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 GHMM

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Nov 2;12:428.
Fast MCMC sampling for hidden Markov Models to determine copy number variations.
Mahmud MP, Schliep A.

 

G4HMM 1.0.0 – G-quadruplex Motif Search using Hidden Markov Models

G4HMM 1.0.0

:: DESCRIPTION

G4HMM is a software of using hidden Markov models to investigate G-quadruplex motifs in genomic sequences

::DEVELOPER

Yuki Kato

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 G4HMM

:: MORE INFORMATION

Citation

BMC Genomics. 2014;15 Suppl 9:S15. doi: 10.1186/1471-2164-15-S9-S15. Epub 2014 Dec 8.
Using hidden Markov models to investigate G-quadruplex motifs in genomic sequences.
Yano M, Kato Y.

HaploHMM 20140622 – Hidden Markov Model (HMM) Based Program for Haplotype Inference

HaploHMM 20140622

:: DESCRIPTION

HaploHMM is a Hidden Markov Model (HMM) based program for haplotype inference using identified haplotypes and haplotype patterns

::DEVELOPER

Kui Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 HaploHMM

:: MORE INFORMATION

Citation

Front Genet. 2014 Aug 12;5:267. doi: 10.3389/fgene.2014.00267. eCollection 2014.
A hidden Markov model for haplotype inference for present-absent data of clustered genes using identified haplotypes and haplotype patterns.
Wu J, Chen GB, Zhi D, Liu N, Zhang K.

NovoHMM – hidden Markov model for de novo Peptide Sequencing

NovoHMM

:: DESCRIPTION

NovoHMM is a software for hidden Markov model for de novo peptide sequencing.

::DEVELOPER

Bernd Fischer

:: SCREENSHOTS

NovoHMM

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 NovoHMM

:: MORE INFORMATION

Citation

Anal Chem. 2005 Nov 15;77(22):7265-73.
NovoHMM: a hidden Markov model for de novo peptide sequencing.
Fischer B, Roth V, Roos F, Grossmann J, Baginsky S, Widmayer P, Gruissem W, Buhmann JM.

Hammock v1.2.0 – Hidden Markov Model-based Peptide Clustering algorithm

Hammock v1.2.0

:: DESCRIPTION

Hammock is a tool for peptide sequence clustering. It is able to cluster extremely large amounts of short peptide sequences into groups sharing sequence motifs.

::DEVELOPER

REGIONAL CENTRE FOR APPLIED MOLECULAR ONCOLOGY (RECAMO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Java
  • Clustal Omega
  • Hmmer3
  • HHsuite

:: DOWNLOAD

 Hammock

:: MORE INFORMATION

Citation:

Hammock: A Hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets.
Krejci A, Hupp T, Lexa M, Vojtesek B, Muller P.
Bioinformatics. 2015 Sep 5. pii: btv522

PRED-TMBB – Predicting and discriminating beta-barrel outer membrane proteins with Hidden Markov Models

PRED-TMBB

:: DESCRIPTION

PRED-TMBB is a web server for predicting the topology of beta-barrel outer membrane proteins.

::DEVELOPER

The Biophysics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PRED-TMBB: a web server for predicting the topology of beta-barrel outer membrane proteins.
Bagos PG, Liakopoulos TD, Spyropoulos IC, Hamodrakas SJ.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W400-4.

VIPR 2.0 / VIPR HMM – Viral Identification with a PRobabilistic Algorithm / Hidden Markov Model

VIPR 2.0 / VIPR HMM

:: DESCRIPTION

VIPR is a software tool for analyzing diagnostic microarrays. The VIPR algorithm is based on a Bayesian statistical framework and requires a training set of positive control hybridizations representing the desired diagnostic targets. The advantage of a probabilistic algorithm in this context is that the positive control data can be used to improve classification of unknown infections. VIPR version 2.0 also includes functionality for detecting recombinant viruses using a hidden Markov model.

VIPR HMM is a hidden Markov model for detection recombination with microbial detection microarrays.

::DEVELOPER

Wanglab , Washington University School of Medicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 VIPR / VIPR HMM

:: MORE INFORMATION

Citation:

VIPR HMM: a hidden Markov model for detecting recombination with microbial detection microarrays.
Allred AF, Renshaw H, Weaver S, Tesh RB, Wang D.
Bioinformatics. 2012 Nov 15;28(22):2922-9. doi: 10.1093/bioinformatics/bts560.

VIPR: A probabilistic algorithm for analysis of microbial detection microarrays.
Allred AF, Wu G, Wulan T, Fischer KF, Holbrook MR, Tesh RB, Wang D.
BMC Bioinformatics. 2010 Jul 20;11:384. doi: 10.1186/1471-2105-11-384.

XHMM 20140711 – eXome-Hidden Markov Model

XHMM 20140711

:: DESCRIPTION

The XHMM C++ software suite was written to call copy number variation (CNV) from next-generation sequencing projects, where exome capture was used (or targeted sequencing, more generally).

::DEVELOPER

Purcell Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 XHMM

:: MORE INFORMATION

Citation

Using XHMM Software to Detect Copy Number Variation in Whole-Exome Sequencing Data.
Fromer M, Purcell SM.
Curr Protoc Hum Genet. 2014 Apr 24;81:7.23.1-7.23.21. doi: 10.1002/0471142905.hg0723s81.