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Protocols

diChIPMunk specifications

Information


Unique identifier OMICS_00481
Name diChIPMunk
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A DNA sequence
Output data DiChIPMunk converts all DNA sequences from mono to dinucleotide alphabet. Each dinucleotide is constructed from two single neighboring nucleotide letters.
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 4.3
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Ivan Kulakovskiy

Publication for diChIPMunk

diChIPMunk citations

 (4)
library_books

Combining phylogenetic footprinting with motif models incorporating intra motif dependencies

2017
BMC Bioinformatics
PMCID: 5333389
PMID: 28249564
DOI: 10.1186/s12859-017-1495-1

[…] ndencies have been shown to outperform simpler motif models like the PWM model [–]. Examples for highly popular tools that model intra-motif dependencies are Dimont [], MEME-ChIP [], DeepBind [], and diChIPMunk [].In contrast, the second group of de-novo motif discovery approaches known as phylogenetic footprinting incorporates orthologous sequences of at least two phylogenetically related species […]

call_split

Architectural proteins Pita, Zw5,and ZIPIC contain homodimerization domain and support specific long range interactions in Drosophila

2016
Nucleic Acids Res
PMCID: 5009728
PMID: 27137890
DOI: 10.1093/nar/gkw371
call_split See protocol

[…] as done using MACS2 () (https://github.com/taoliu/MACS) against preimmune and input control data. Peak sets obtained with the preimmune control were smaller and were utilized for motif discovery with diChIPMunk (,). Resulting dinucleotide position weight matrices were used for motif finding in peaks obtained with the input control. To detect peaks with strong motif occurrences, we estimated a P-va […]

call_split

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP Seq data

2014
BMC Genomics
PMCID: 4234207
PMID: 24472686
DOI: 10.1186/1471-2164-15-80
call_split See protocol

[…] e of pattern matching and pattern detection approaches for TFBS prediction in the context of ChIP-Seq data, we applied oPWM and SiteGA (as representatives of the former class) as well as ChIPMunk and diChIPMunk (as representatives of the latter class) to analyze a dataset of 4455 FoxA2-binding loci (ChIP-Seq peaks with read coverage of at least 15) in mouse adult liver chromatin [].To produce a su […]

library_books

A general approach for discriminative de novo motif discovery from high throughput data

2013
Nucleic Acids Res
PMCID: 3834837
PMID: 24057214
DOI: 10.1093/nar/gkt831

[…] otif order 1 than for motif order 0 for at least one combination of training and test data sets in Supplementary Figure S5–S13, and we compare the dependencies detected by Dimont to those detected by diChIPMunk () in Section 6 of the Supplementary Material. […]

Citations

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diChIPMunk institution(s)
Laboratory of Bioinformatics and Systems Biology, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia; Department of Computational Systems Biology, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Laboratory of Molecular Genetics Systems, Institute of Cytology and Genetics of the Siberian Division of Russian, Academy of Sciences, Novosibirsk, Russia; Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk, Russia; Laboratory of Regulation of Gene Expression, Institute of Cytology and Genetics of the Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia; Yandex Data Analysis School, Data Analysis Department, Moscow Institute of Physics and Technology, Moscow, Russia; State Research Institute of Genetics and Selection of Industrial Microorganisms, Moscow, Russia; Moscow Institute of Physics and Technology, Moscow, Russia
diChIPMunk funding source(s)
This work was supported by a Dynasty Foundation Fellowship; Russian Foundation for Basic Research [12-04-32082] and [12-04-01736]; Presidium of the Russian Academy of Sciences program in Cellular and Molecular Biology; Presidium of the Russian Academy of Sciences Fundamental Research Subprogram “Gene pools dynamics and conservation”; Russian Federation Government Contract 8088 under program “Scientific and pedagogical personnel of innovative Russia”.

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