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Free software for motif finding/prediction based on free energy calculations. Run as perl scripts to that call the package. Can be used for motif prediction in RNA or DNA and is capable of converting between the two, default is RNA. Primary author Joshua Starmer.
Links to sites that run the software or where it can be obtained
Obtainable on SourceForge
Hardware/Software requirements, if applicable
Usage information and options can be viewed by type the name of the script followed by -h.
$ perl free_align.pl -h
- Starmer, J et al. (2006) Predicting Shine-Dalgarno sequence locations exposes genome annotation errors. PLoS Comput. Biol. 2 e57 PubMed