PuFFIN specifications


Unique identifier OMICS_16753
Alternative name Positioning for Fuzzy and FIxed Nucleosomes
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The input file for the tool should contain the reads only for considered chromosome (contig).
Input format BED
Operating system Unix/Linux
Programming languages Python
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes




No version available


  • person_outline Anton Polishko

Publication for Positioning for Fuzzy and FIxed Nucleosomes

PuFFIN citation


DNA encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum

BMC Genomics
PMCID: 4035074
PMID: 24885191
DOI: 10.1186/1471-2164-15-347

[…] Nucleosome positions and score were computed using our novel nucleosome positioning software tool PuFFIN []. PuFFIN is a multi-scale peak-calling method that replaces each nucleosome-enriched paired-end sequence read with a Gaussian curve. By summing these Gaussian distributions for all paired-en […]

PuFFIN institution(s)
Department of Computer Science and Engineering, University of California, Riverside, CA, USA; Department of Cell Biology and Neuroscience, University of California, Riverside, CA, USA
PuFFIN funding source(s)
This study was financially supported by the Human Frontier Science Program [grant LT000507/2011-L]; the National Institutes of Health [grant R01 AI85077-01A1]; and the National Science Foundation [grant IIS-1302134].

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