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.

APOLLOH 0.1.1 – HMM for Profiling Loss of Heterozygosity in Whole Cancer Genome Shotgun Sequencing data

APOLLOH 0.1.1

:: DESCRIPTION

APOLLOH is a hidden Markov model (HMM) for predicting somatic loss of heterozygosity and allelic imbalance in whole tumour genome sequencing data.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Matlab

:: DOWNLOAD

 APOLLOH

:: MORE INFORMATION

Citation

G. Ha, A. Roth, D. Lai, A. Bashashati, J. Ding, R. Goya, R. Giuliany, J. Rosner, A. Oloumi, K. Shumansky, S.-F. Chin, G. Turashvili, M. Hirst, C. Caldas, M. A. Marra, S. Aparicio, S. P. Shah.
Integrative analysis of genome-wide loss of heterozygosity and mono-allelic expression at nucleotide resolution reveals disrupted pathways in triple negative breast cancer.
Genome Research 2012, 2012 Oct;22(10):1995-2007.

hiddenDomains 2.2 – A modern HMM to Identify ChIP-seq Enrichment

hiddenDomains 2.2

:: DESCRIPTION

hiddenDomains uses a Hidden Markov Model to identify enriched domains in ChIP-seq data. It accepts BAM files for input and can perform an analysis with or without control data. The output is a BED file, ready for the UCSC genome browser, that contains the domains and is color coded according to their posterior probabilities.

::DEVELOPER

hiddenDomains team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux/ MacOsX
  • Perl
  • R

:: DOWNLOAD

 hiddenDomains

:: MORE INFORMATION

Citation

Detecting broad domains and narrow peaks in ChIP-seq data with hiddenDomains.
Starmer J, Magnuson T.
BMC Bioinformatics. 2016 Mar 24;17(1):144. doi: 10.1186/s12859-016-0991-z.

HHCompare – HMM based protein Hierarchical Clustering

HHCompare

:: DESCRIPTION

HHCompare is a pipeline for HMM-HMM comparison based hierarchial clustering and analysis of potential paralogues in sequence set.

::DEVELOPER

Ranko Gacesa, King’s College London

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 HHCompare

:: MORE INFORMATION

Citation

Gene duplications are extensive and contribute significantly to the toxic proteome of nematocysts isolated from Acropora digitifera (Cnidaria: Anthozoa: Scleractinia).
Gacesa R, Chung R, Dunn SR, Weston AJ, Jaimes-Becerra A, Marques AC, Morandini AC, Hranueli D, Starcevic A, Ward M, Long PF.
BMC Genomics. 2015 Oct 13;16(1):774. doi: 10.1186/s12864-015-1976-4.

Marcoil 1.2 – HMM-based Coiled-coil Prediction program

Marcoil 1.2

:: DESCRIPTION

MARCOIL is a hidden MARkov model-based program that predicts existence and location of potential coiled-coil domains in protein sequences.

::DEVELOPER

Mauro Delorenzi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

MARCOIL

:: MORE INFORMATION

Citation:

Bioinformatics. 2002 Apr;18(4):617-25.
An HMM model for coiled-coil domains and a comparison with PSSM-based predictions.
Delorenzi M, Speed T.

HUF-ZINC – HMM-based U-shape Motif Finder for Zinc Binding

HUF-ZINC

:: DESCRIPTION

HUF-ZINC is a HMM-based web server for prediction of the novel, as well as conventional, zinc finger motifs in protein sequences.

::DEVELOPER

Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Bioinform Comput Biol. 2013 Feb;11(1):1340008. doi: 10.1142/S0219720013400088. Epub 2013 Jan 16.
Motif discovery with data mining in 3D protein structure databases: discovery, validation and prediction of the U-shape zinc binding (“Huf-Zinc”) motif.
Maurer-Stroh S1, Gao H, Han H, Baeten L, Schymkowitz J, Rousseau F, Zhang L, Eisenhaber F.

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.

HINT 0.1.1 – Hmm-based IdeNtification of Tf footprints

HINT 0.1.1

:: DESCRIPTION

HINT integrates both DNase I hypersensitivity and histone modifications for the detection of open chromatin regions and active binding sites.

::DEVELOPER

IZKF Computational Biology and Bioinformatics Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 HINT

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Nov 15;30(22):3143-51. doi: 10.1093/bioinformatics/btu519. Epub 2014 Aug 1.
Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications.
Gusmao EG, Dieterich C, Zenke M, Costa IG

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

zipHMM 1.0.1 – A highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm

zipHMM 1.0.1

:: DESCRIPTION

zipHMM is a library for hidden Markov models that exploits repetitions in strings to greatly speed up the calculations of the log likelihood of a sequence.

::DEVELOPER

Thomas Mailund

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  zipHMM

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2013 Nov 22;14:339. doi: 10.1186/1471-2105-14-339.
zipHMMlib: a highly optimised HMM library exploiting repetitions in the input to speed up the forward algorithm.
Sand A1, Kristiansen M, Pedersen CN, Mailund T.