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