GeSICA: Genome Segmentation from Intra-Chromosomal Associations

contact: gesica [dot] tongji [at] gmail [dot] com


Useful Files



Human Genome Segmentation with GeSICA

Welcome to the website of GeSICA, a genome segmentation software.


GeSICA is a two-step strategy of segmenting the human genome into detailed genomic organizational units. In the first step, GeSICA calculates Interaction Ratio of each genomic bin to dichotomize the human genome into two types of states. Only the functional-related regions are taken into account in the second step -- Markov Cluster Algorithm (MCL). And a number of clusters are thus generated. Finally, three types of files are generated as the output of GeSICA: the Interaction-Ratio wiggle file, the segmentation bed file and the MCL genomic clusters file. Please see the publication for more details about the algorithms and the latest README for information regarding installation and usage.

Please cite: Liu L, Zhang Y, Feng J, Zheng N, Yin J, Zhang Y. GeSICA: genome segmentation from intra-chromosomal associations. BMC Genomics 2012; 13:164.


Change Log

9 Jan 2012
Rename a parameter "block" to "cluster" and revise the README file.

Change Log

30 Sep 2011
Fix a bug in a mouse genome version(mm9).

18 Aug 2011
Website is up
Please Note that the website and public code is still well under development.
The GeSICA-Alpha code is currently written in Python.

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