Sufficache is a python module for fast Extended Suffix Array search for transcription factor binding sites. It is primarily an implementation of algorithms described in the following papers:
- Beckstette, M. et al. (2006). ”Fast index based algorithms and software for matching position specific scoring matrices”. BMC Bioinformatics 7: 389. DOI:10.1186/1471-2105-7-389. PMC 1635428. PMID 16930469, and
- Juha Kärkkäinen, Peter Sanders and Stefan Burkhardt. Linear work suffix array construction. J. ACM, 53 (6), pp. 918-936, 2006.
In particular, a faster implementation of the suffix array construction algorithm is gratefully borrowed from the pysuffix project (http://code.google.com/p/pysuffix/).