tfPatterns is a standalone java tool that mimics GCG Findpatterns by reading tfsites.gcg files (IFTI) to identify potential TF binding sites in a nucleotide sequence, but is based on an algorithm similar to IFTI Tfsitescan. Accelrys has created a wrapper that allow users to run tfPatterns analyses as a Pipeline Pilot Sequence Analysis Collection component. tfPatterns has an option to write GFF3 files instead of Findpatterns output files, so that tfPatterns analysis results can be immediately viewed in an interactive graphic form by Pipeline Pilot's GFF3 readers. A demo version of this Pipeline Pilot component with example protocol can be downloaded here. The protocol is configured to run with sample data packaged with the Sequence Analysis Collection. Place the IFTI folder that is contained in the zip file into your PP user directory. The example should run as is.

For a fully functional version of tfPatterns with updated tfsites.gcg files (07/31/08), contact David Ghosh whose contact information is shown below.

David Ghosh, PhD
President/Director
Institute for Transcriptional Informatics
Woodland Hills, CA 91365
Telephone: 412-682-0550
Website: http://www.ifti.org/

Submitted by Nancy Latimer (ACCL)