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diChIPMunk

A computational tool that constructs transcription factor binding sites TFBS models as optimal dinucleotide PWMs, thus accounting for correlations between nucleotides neighboring in input sequence. ChIPMunk can account for ChIP-Seq base coverage data, i.e. use the shape of ChIP-Seq tags pileup as prior positional information for probable locations of binding sites within extended ChIP-Seq peak sequence.

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diChIPMunk forum

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diChIPMunk classification

diChIPMunk specifications

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

diChIPMunk distribution

versioning

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No versioning.

diChIPMunk support

Documentation

Maintainer

  • Ivan Kulakovskiy <>

Credits

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Publications

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

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”.

Link to literature

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