MotifFinder
MotifFinder is a GUI-based Windows program that will analyze your FASTA file and the modifications.gff file output by kineticsTools or SMRT Portal and report motifs discovered.
MotifFinder version 21 (1 MB)
Instructions Unzip the package, and execute the setup.exe link. The program runs from the zip directory - it does not install itself on your machine. Provide a link or filesystem path to the reference FASTA file and the modifications.gff.gz file produced by SMRT Portal, select a modification QV threshold, then click the 'Run Motif Finding' button. Results will appear in a new tab on the main window. You can run multiple motif find jobs with different settings. They will each appear in a new tab.
MotifFinder also is able to calculate statistics based off of a user entered motif. After the initial analysis, on the "Motif Finding Job" page, click on the button titled "Input an Additional Motif to Analyze":
