Tag: HMM

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

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.

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.

HAPAA 1.0 – HMM-based Analysis of Polymorphisms in Admixed Ancestries

HAPAA 1.0

:: DESCRIPTION

HAPAA is a novel approach for ancestry inference that models the allelic and haplotypic variation in the populations and captures the signal of correlation due to linkage disequilibrium, resulting in greatly improved accuracy.

::DEVELOPER

Serafim’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 HAPAA

:: MORE INFORMATION

Citation

Genome Res. 2008 Apr;18(4):676-82. doi: 10.1101/gr.072850.107.
Effect of genetic divergence in identifying ancestral origin using HAPAA.
Sundquist A, Fratkin E, Do CB, Batzoglou S.

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.

HMMcopy 0.1.1 – HMM for Detecting Somatic Copy Number alterations in tumour-normal paired Whole Genome Sequencing data

HMMcopy 0.1.1

:: DESCRIPTION

HMMcopy is a suite of tools to make copy number estimations for whole genome data with GC and mappability correction, then segment and classify copy number profiles with a robust Hidden Markov Model. Designed to work with high coverage whole genome HTS data, it can derive copy number estimations from large (~250GB) aligned BAM files in 2 hours on a single core with minimal memory requirements.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R package

:: DOWNLOAD

 HMMcopy

:: 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 Oct;22(10):1995-2007.

PathRacer 3.15.0 – Racing Profile HMM Paths on Assembly Graph

PathRacer 3.15.0

:: DESCRIPTION

PathRacer is a novel standalone tool that aligns profile HMM directly to the assembly graph (performing the codon translation on fly for amino acid pHMMs). The tool provides the set of most probable paths traversed by a HMM through the whole assembly graph, regardless whether the sequence of interested is encoded on the single contig or scattered across the set of edges, therefore significantly improving the recovery of sequences of interest even from fragmented metagenome assemblies.

::DEVELOPER

Center for Algorithmic Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  MacOsX
  • Python

:: DOWNLOAD

PathRacer

:: MORE INFORMATION

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.

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.

hiddenDomains 3.1 – A modern HMM to Identify ChIP-seq Enrichment

hiddenDomains 3.1

:: 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.