ChIPMunk statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left De novo motif discovery chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

ChIPMunk specifications

Information


Unique identifier OMICS_02140
Name ChIPMunk
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 4.3
Stability Stable
Requirements
Java Runtime Environment
Maintained Yes

Versioning


Add your version

Maintainer


  • person_outline Ivan Kulakovskiy <>

Information


Unique identifier OMICS_02140
Name ChIPMunk
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 3.2a
Stability Stable
Maintained Yes

Maintainer


  • person_outline Ivan Kulakovskiy <>

Publication for ChIPMunk

ChIPMunk in publications

 (13)
PMCID: 5727025
PMID: 29233972
DOI: 10.1038/s41467-017-01070-w

[…] significantly activate the il9 and il21 promoters, which raised the assumption that a partner is needed (fig. ). to better document the function of irf8 during th9 cell differentiation, we used the chipmunk tool and the meme-chip tool to characterise the irf8-binding sequence. we identified the 5ʹ-tbtstbtvtktbtbt-3ʹ motif as most often represented in our irf8 chip-seq experiment (fig. ). […]

PMCID: 5438342
PMID: 28526842
DOI: 10.1038/s41598-017-02110-7

[…] of ompr from 25 binding peaks (kwwgttacat) was consistent with the previously characterized repeat sequence of the ompr-binding site (tttgttacat) (fig. ). in addition, we used two other methods, chipmunk and dichipmunk, to identify dna sequence motifs of ompr–. the identified sequence motifs were similar to that from the meme software tool in that these two methods generated the previously […]

PMCID: 4509496
PMID: 26236718
DOI: 10.1155/2015/218068

[…] has advantageous to deal with the (l,  d) motif finding in the chip-seq data; meanwhile it also demonstrates better performance than other current widely-used algorithms such as meme, weeder, chipmunk, and dreme., a transcription factor (tf) binds to the specific dna sequences, which carries the information of the transcription and gene expressions. hence locating the transcription factor […]

PMCID: 4337573
PMID: 25691594
DOI: 10.1128/mBio.02352-14

[…] and prokaryote or e. coli as the input motif database. the consensus bola binding motif was further confirmed using other motif search software, such as rsat oligo-analysis (), completemotifs (), chipmunk (), and dreme (). additionally, the determined sequence was tested by inverted motif search using rsat dna pattern matching software ()., β-galactosidase activity assays were performed […]

PMCID: 4265420
PMID: 25442502
DOI: 10.1186/1471-2164-15-1047

[…] need to be identified by a motif-finding tool [, ]. although a few new motif-finders have been developed to analyze large sequence sets from chip-seq experiments, such as seeder [], trawler [, ], chipmunk [], hms [], cmf [], steme [], dreme [], decod [], rsat [], and posmo [], they are typically used to find the cres of a chip-ed tf in a short region of sequences (~200 bp) around the binding […]


To access a full list of publications, you will need to upgrade to our premium service.

ChIPMunk institution(s)
Research Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia; Institut Curie, Paris, France; INSERM, U900, Paris, France; INSERM, U830, Paris, France; Mines ParisTech, Fontainebleau, France; Johns Hopkins University, Baltimore, MD, USA; Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
ChIPMunk funding source(s)
Supported by Russian Federal Agency for Science and Innovation State Contract [02.531.11.9003, 02.740.11.5008]; Russian Fund for Basic Research Project [10-04-92663].

ChIPMunk reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ChIPMunk