What is storm?
The Search Tool for Occurrences of Regulatory Motifs, or storm , is an algorithm for scanning through sequences to find transcription factor binding sites represented as position frequency matrices.
What is modstorm?
modstorm is an extension of the storm software to search for modules of transcription factor binding sites.
Why should I use storm?
If you are searching through many sequences for transcription factor binding sites, and speed is an issue, we recommend using storm . storm creates suffix trees of the sequences to be searched to provide efficient scanning. Furthermore, storm provides multiple, rigorous methods to assess the statistical significance of motif occurrences.
Why should I use modstorm?
If you are searching through many sequences for modules of transcription factor binding sites, we recommend using modstorm . In addition to providing efficient scanning as with storm , modstorm allows for the calculation of statistical significance of module matches.
What do all these options mean?
We have tried to explain each of the options in storm and modstorm on the storm examples and modstorm examples pages.
What do I need to run these programs
The requirements to run storm and formattable are listed here .
How are the gk-table files created?
The gk-tables provided at are created with the formattable program provided as part of the CREAD software package. The files that are provided consist of gk-tables constructed for Human, Mouse and Rat promoters of three sizes: small (-500 to +100 w.r.t. TSS), medium (-1000 to +300 w.r.t. TSS) and large (-5000 to +500 w.r.t. TSS). The promoter sequences used to construct the promoter gk-tables were obtained from the CSHL mammalian promoter database .
Can I make my own gk-table?
We provide the formattable software for people who are interested in constructing gk-tables from sequences other than what we provide.
I found a bug
Send an e-mail to dschones at cshl dot edu
Got another question?
Send an e-mail to dschones at cshl dot edu