Beckstette, Michael; Homann, Robert; Giegerich, Robert; Kurtz, Stefan: Fast index based algorithms and software for matching position specific scoring matrices. In: BMC Bioinformatics. Jg.7 H. 1. 2006
Inhalt
- Background
- Results
- PSSMs and lookahead scoring: LAsearch
- PSSM searching using enhanced suffix arrays: ESAsearch
- Performance improvements via alphabet transformations
- Finding an appropriate threshold for PSSM searching: LazyDistrib
- Probabilities and expectation values
- Calculation of exact PSSM score distributions
- Evaluation with dynamic programming
- Restricted probability computation
- Lazy evaluation of the permuted matrix
- Implementation and computational results
- Discussion and conclusion
- Availability
- Authors' contributions
- Acknowledgements
- References