-
Notifications
You must be signed in to change notification settings - Fork 2
Position-sensitive word-set DNA motif finder
License
iwd32900/powrs
Folders and files
Name | Name | Last commit message | Last commit date | |
---|---|---|---|---|
Repository files navigation
POWRS - the POsition-sensitive WoRd Set motif finder ==================================================== Developed by Ian W. Davis and GrassRoots Biotechnology Terms of use are in LICENSE.txt. Installation instructions are in INSTALL.txt. Instructions for use can be obtained by running python powrs.py --help from this directory once dependencies are installed. Sample data for the CREB transcription factor in the paper has been included. To reproduce that analysis, do cd sample_data python ../powrs.py --window-width 50 --length 2000 --improve-limit 800 CREB.in.fa.gz CREB.out.fa.gz > CREB.powrs.txt The final results of the algorithm will be at the end of this (large) text file, below the final double line (=============). See the --help text for instructions on interpretting the output. DEVELOPMENT HISTORY =================== * Version 1.2 21 Mar 2013 Updated release that adds binning to correct for sequence composition bias (--bins, in the style of Amadeus) and searching with a fixed-size gap in the middle of the motif (--midgap). The scoring function changed subtly to enable binning, but rank orderings of motifs should change very little. * Version 1.1 24 May 2012 Updated release that adds multi-processor support (--parallel) and (experimental!) support for clustering similar motifs in a post-processing step. The main algorithm is unchanged, and pre-clustering results should be identical. * Version 1.0 7 Nov 2011 Initial release of the code. This is the code referenced by the paper, and should be used to reproduce any analysis from that work.
About
Position-sensitive word-set DNA motif finder
Resources
License
Stars
Watchers
Forks
Releases
No releases published
Packages 0
No packages published