diChIPMunk 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
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Documentation
Maintainer
- person_outline Ivan Kulakovskiy <>
Publication for diChIPMunk
library_books
From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites.
2013 J Bioinform Comput Biol
PMID: 23427986
diChIPMunk IN pipeline
2016
PMCID: 5009728
PMID: 27137890
DOI: 10.1093/nar/gkw371
[…] done using macs2 (62) (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 (63,64). 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 […]
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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