PscanChIP

PscanChIP is a web server that is a valuable tool for bioinformaticians, geneticists, and molecular biologists. It assists in analyzing regions identified from a Chromatin immunoprecipitation followed by sequencing with next-generation technologies (ChIP-Seq) experiment. The tool is instrumental in determining the actual DNA-binding sites for a given transcription factor (TF).

The regions identified from a ChIP-Seq experiment often require further analysis to determine the actual DNA-binding sites for the TF. PscanChIP addresses this challenge by using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices or descriptors uploaded by users. It evaluates motif enrichment and positional bias within the regions according to different measures and criteria.

PscanChIP is capable of identifying the actual binding sites for the TF investigated by a ChIP-Seq experiment and secondary motifs corresponding to other TFs that tend to bind the same regions. This valuable feature allows for identifying other transcription factors that may be cooperating or interacting with the TF in transcription regulation.

The tool can also identify precise positional correlations among the respective sites. The web interface is free for use, with no login required. This makes it accessible to anyone who needs to analyze genomic regions derived from a ChIP-Seq experiment.