Computational protocol: Chromatin domain boundary element search tool for Drosophila

Similar protocols

Protocol publication

[…] The cdBEST algorithm is implemented in Perl as two variants, the cdBEST basic and advanced. The basic version is a command line script requires Perl alone, can be used in Linux and Mac computers directly without any additional requirements. cdBEST_basic uses FASTA formatted sequence files for boundary search and produces text output files. The advanced version has a simple GUI (graphical user interface), where user can choose various parameters for searching boundaries. In addition to text files, this version produces an image output showing boundaries and gene annotations together with the scale for easy correlation. cdBEST_advanced requires Perl-Tk module for generating GUI and BioPerl modules () to draw image output files. In addition cdBEST search results can be uploaded to various genome browsers such as FlyBase GBrowse and UCSC genome Browser as custom tracks to view along with any other feature. The cdBEST source file for different OS platforms with a readme file is available for download at http://www.ccmb.res.in/rakeshmishra/cdBEST.html. […]

Pipeline specifications

Software tools BioPerl, GBrowse
Databases FlyBase UCSC Genome Browser
Applications ChIP-on-chip analysis, Genome data visualization
Organisms Drosophila melanogaster