Designed by  Adam Wenick, Henry Bigelow, Allan Wong, and Oliver Hobert
Implemented by Henry Bigelow

CisOrtho is a software pipeline for finding binding sites for a transcription factor, based on a user-defined set of known binding sites. It proceeds in five steps:

• Build a Position Weight Matrix (PWM) using HMMER software from a user-provided multiple ungapped alignment of transcription factor binding sites.



• Isolate and classify non-exonic genomic sequence from C. elegans and C. briggsae based on gene model annotations in GFF (General Feature Format) files.



• Search through the C. elegans and C. briggsae regions, finding the top N hits (also user provided)



• Filter out high-scoring hits in one species which don't have a high-scoring hit for the corresponding orthologue in the other species (Phylogenetic Footprinting)



• Output results sorted according to different criteria in a webpage with links to Wormbase Gene models

Please see the User Manual for a thorough description of its usage and design.