SimSearch is an IGB http://bioviz.org/igb/ plugin to identify and compare occurrences of (epi)genomics feature patterns in multiple genome browser tracks.

It is based on a pattern-search algorithm that provides biologists with the ability, once they identify an interesting genomic pattern, to look for similar occurrences in the data, thus facilitating genomic data access and use. For example, such patterns can describe gene expression regulatory DNA areas including heterogeneous (epi)genomic features (e.g. histone modification and/or different transcription factor binding regions). It is possible to define complex patterns based on perfect matches in genome tracks (regions that must match), partial matches (regions that are allowed to be absent), and negative matches (for instance to search for regions distant from transcription start sites).

The SimSearch algorithm has been developed through a collaboration between University of Bologna and Politecnico di Milano, and is included in the SimSearch App as part of the [DATA-DRIVEN GENOMIC COMPUTING (GeCo)] http://www.bioinformatics.deib.polimi.it/geco/ project.

The SimSearch App for IGB is developped by @arnaudceol for the Istituto Italiano di Tecnologia.

For more information, documentation and example, look at the [SimSearch project URL] https://deib-geco.github.io/simsearch/, or this [WIKI] https://github.com/DEIB-GECO/simsearch/wiki for a quick installation guide.

** Quickstart: **

To compile the plugin and create a local repository:

mvn initialize clean bundle-markdown-encoder:encodeMarkdown install bundle:index