MoSDi (Motif Statistics and Discovery) contains a lot of sequence analysis algorithms, including methods for
- motif statistics, e.g. compute the exact occurrence count distribution of a motif,
- exact motif discovery: extraction of motifs with provably optimal p-value,
- analysis of pattern matching algorithms: compute (for given algorithm and pattern) the exact distribution of the number of character accesses caused by searching a random text,
- statistics of fragment masses resulting from proteolytic cleavage of proteins,
- computing the expectated read length of sequencing reads for a given dispensation order (for 454 or IonTorrent),
- analysing sensitivity of spaced alignment seeds.
- Linux / MacOsX / Windows
:: MORE INFORMATION
IEEE/ACM Trans Comput Biol Bioinform. 2012 Nov-Dec;9(6):1737-50.
Probabilistic arithmetic automata and their applications.
Marschall T, Herms I, Kaltenbach HM, Rahmann S.