ChIPMunk
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Application data |
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| Created by | Kulakovskiy IV, Boeva VA, Favorov AV, Makeev VJ |
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| Biological application domain(s) | ChIP-seq, Sequence motifs |
| Principal bioinformatics method(s) | Sequence motif comparison, Sequence motif discovery |
| Created at | Engelhardt Institute of Molecular Biology RAS
Vavilov Institute of General Genetics RAS |
| Maintained? | Yes |
| Input format(s) | multi-fasta, extended multi-fasta |
| Output format(s) | plain text |
| Software features | efficient motif discovery for huge datasets up to tens of thousands of sequences; multi-core CPU support; usage of the ChIP-seq base coverage peak data |
| Programming language(s) | Java |
| Licence | Freeware |
| Operating system(s) | platform-independent |
Summary: ChIPMunk is a fast heuristic DNA motif digger based a on greedy approach accompanied by bootstrapping. ChIPMunk identifies the strong motif with the maximum Kullback Discrete Information Content in a given set of DNA sequences.
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Description
ChIPMunk [1] is a fast heuristic DNA motif digger based on greedy approach accompanied by bootstrapping. ChIPMunk identifies the strong motif with the maximum Discrete Information Content in a set of DNA sequences. ChIPMunk uses (extended) multifasta as the input format and supports IUPAC DNA letters in the input sequences.
ChIPMunk can integrate data from different sources including ChIP-chip to produce improved binding motifs with better sensitivity and specificity.
Independent benchmarks have shown that the overall quality of the ChIPMunk motifs is better or comparable to the well-known tools while the speed remains quite acceptable.
Links
References
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