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    Tool Name:  

iNPS   Downloaded: 0   Viewed: 0
Developed By: Department of Molecular Systems Biology


iNPS is a widely used software package for detecting nucleosome positions from MNase-seq data, but its accuracy needs much improvement. We developed the improved NPS (iNPS) algorithm by adding two major modifications to NPS to precisely determine the boundary of nucleosomes and to merge or separate shoulder peaks based on their relationship to neighboring major peaks. iNPS achieved significantly better performance compared with NPS: it unambiguously detects 60% more nucleosomes; the detected nucleosomes display significantly more uniform distributions of nucleosome ’widths’ and neighboring center-center distances, give rise to sharper wave-like patterns and better phasing of average nucleosome profiles at key regulatory regions, and show higher consistency between independent subsets of input data than NPS. Furthermore, iNPS identifies sharper nucleosome profiles with higher quality and lower false positive rates than other published methods. Consequently, only iNPS, but not NPS, detected differentially positioned nucleosomes between resting and activated CD4+ T cells that display clear enrichment for pathways relevant to T cell activation, and enrichment for binding motifs of densely interacting transcription factors. Finally, iNPS has the unique advantage of detecting different types of nucleosomes that are associated with different biological properties based on nucleosome shapes.

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iNPS is developed and maintained by CAS-MPG Partner Institute for Computational Biology(PICB) ,Chinese Academy of Sciences. The software is only free of charge for non-commercial users.



    Contact Information:  

If you have any feedback or question concerning the tools you can further click the Project Website , or please feel free to contact us at jdhanpicb.ac.cn.