Sissrs

Application data
Created by	Raja Jothi, National Institutes of Health (NIH)
Biological application domain(s)	ChIP-seq
Principal bioinformatics method(s)	Peak calling
Maintained?	Maybe
Input format(s)	BED
Output format(s)	BED, WIG
Programming language(s)	Perl
Operating system(s)	Linux, UNIX

Summary: Produce a list of peakmaxima from aligned positions.

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SISSRs is a software application for precise identification of genome-wide transcription factor binding sites from ChIP-seq data. It is essentially a perl implementation of the SISSRs algorithm outlined in Jothi et al [1], with several new features that were not fully described in the original paper. ChIP-seq, which combines chromatin immunoprecipitation (ChIP) with next generation massively parallel sequencing, is a powerful experimental technique to determine whether proteins including, but not limited to, transcription factors bind to specific regions on chromatin in vivo. In ChIP-seq, the DNA fragments obtained from ChIP are directly sequenced using the next generation genome sequencers such as Illumina Genome Analyzers. Although the lengths of the input DNA could be anywhere between ~200 bp and 1 kb, typically, only the first 25–50 nt from the DNA ends are sequenced. The resulting short reads are mapped back to a reference genome, and only those reads that map to an unique genomic locus in the reference genome are considered for further analysis. Mapped reads are commonly referred to as tags (henceforth, ‘reads’ and ‘tags’ are used interchangeably). A binding site is a region on the DNA to which specific proteins including, but not limited to, transcription factors bind in vivo. A typical binding site could be anywhere between ~5-20 nucleotides in length.

http://sissrs.rajajothi.com