HMMEditor 1.2 – Visual Editor for Profile Hidden Markov Model

HMMEditor 1.2

:: DESCRIPTION

HMMEditor (HMMVE) is a visual editor for profile Hidden Markov Model (pHMM)

::DEVELOPER

Dr. Jianlin Cheng’s Bioinformatics and Systems Biology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows /MacOsX
  • Java

:: DOWNLOAD

 HMMEditor

:: MORE INFORMATION

Citation

J. Dai and J. Cheng.
HMMEditor: A Visual Editing Tool for Profile Hidden Markov Model.
BMC Genomics. 9(S1):S8, 2008.

HaMStR 13.2.6 – Hidden Markov Model based Search for Orthologs using Reciprocit

HaMStR 13.2.6

:: DESCRIPTION

HaMStR (Hidden Markov Model based Search for Orthologs using Reciprocity)is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HaMStR

:: MORE INFORMATION

Citation:

BMC Evol Biol. 2009 Jul 8;9:157.
HaMStR: profile hidden markov model based search for orthologs in ESTs.
Ebersberger I, Strauss S, von Haeseler A.

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.

Hammock 1.04 – Hidden Markov Model-based Peptide Clustering algorithm

Hammock 1.04

:: 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

AncesHC 2009 – Association Tests by Inferring Ancestral Haplotypes using a Hidden Markov Model

AncesHC 2009

:: DESCRIPTION

AncesHC (ancestral haplotype clustering ) is a program for determining the haplotype structure of a population sample from genotype data, and then testing for association of these haplotypes with either a binary or continous outcome.

::DEVELOPER

Dr Lachlan J Coin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Java

:: DOWNLOAD

 AncesHC

:: MORE INFORMATION

Citation

Shu-Yi Su, David J. Balding and Lachlan J.M. Coin
Disease association tests by inferring ancestral haplotypes using a hidden markov model
Bioinformatics (2008) 24 (7): 972-978.

mCarts 1.2.0 – Hidden Markov model to predict Clustered RNA Motif sites

mCarts 1.2.0

:: DESCRIPTION

mCarts is a hidden Markov model (HMM)-based methods to predict clusters RNA motif sites.

::DEVELOPER

Zhang Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 mCarts

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Aug;41(14):6793-807. doi: 10.1093/nar/gkt421. Epub 2013 May 18.
Prediction of clustered RNA-binding protein motif sites in the mammalian genome.
Zhang C1, Lee KY, Swanson MS, Darnell RB.

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.

TruHmm – TRanscription Unit Assembly by a Hidden Markov model

TruHmm

:: DESCRIPTION

TruHmm is a reference based transcriptome assembler for prokaryotes, and is suitable for assembling transcripts for directional RNA-seq library.

::DEVELOPER

Dr. Su’s lab at the University of North Carolina at Charlotte.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /Windows
  • Perl / C++

:: DOWNLOAD

 TruHmm

:: MORE INFORMATION

Citation

BMC Genomics. 2013 Jul 30;14:520. doi: 10.1186/1471-2164-14-520.
Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling.
Li S1, Dong X, Su Z.

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.

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.