SIPeS specifications


Unique identifier OMICS_00462
Name SIPeS
Alternative name Site Identification from Paired-end Sequencing
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Biological technology Illumina
Operating system Unix/Linux
Programming languages C, Shell (Bash)
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Stability Beta
Maintained Yes




No version available


  • person_outline Dabing Zhang

Publication for Site Identification from Paired-end Sequencing

SIPeS citations


CMT: A Constrained Multi Level Thresholding Approach for ChIP Seq Data Analysis

PLoS One
PMCID: 3988018
PMID: 24736605
DOI: 10.1371/journal.pone.0093873

[…] pecifically, the shapes of putative peaks are defined and evaluated to differentiate between random and non-random fragment placements on the genome. Another algorithm for detecting relevant peaks is site identification from paired-end sequencing (SIPeS) , which can be used for identification of binding sites from short reads generated from paired-end Illumina ChIP-Seq technology. Qeseq is another […]


Practical Guidelines for the Comprehensive Analysis of ChIP seq Data

PLoS Comput Biol
PMCID: 3828144
PMID: 24244136
DOI: 10.1371/journal.pcbi.1003326

[…] ecificity (). Although some peak callers support both single and paired-end reads (e.g., MACS), others are specifically designed to improve sensitivity and specificity in paired-end sequencing (e.g., SIPeS ). Existing peak callers have many user-settable parameters that can greatly affect the number and quality of the peaks called. For instance, the enrichment metric for most peak callers, such as […]

SIPeS institution(s)
School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, UK; Bio-X Research Center, Key Laboratory of Genetics & Development and Neuropsychiatric Diseases, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
SIPeS funding source(s)
Supported by the Funds from the National Key Basic Research Developments Program of the Ministry of Science and Technology, PR China (2009CB941500, 2007CB108700), National ‘863’ High-Tech Project (2006AA10A102), National Natural Science Foundation of China (30725022, 90717109 and 30600347), and Shanghai Leading Academic Discipline Project (B205).

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