PoSSuMsearch is a free and easy to use software that provides a significant speedup of database searches with HMMs by search space reduction with PSSM family models.

When searching with a PSSM it is very important to determine a suitable threshold for a PSSM match.

Usually, the user prefers to specify a significance threshold (i.e., an E-value or a p-value) which has to be transformed into an absolute score threshold for the PSSM under consideration.

This can be done by computing the score distribution of the PSSM, using well-known dynamic programming (DP, for short) methods, e.g., [Sta89, WNB00, Rah03, RMV03].

NOTE: PoSSuMsearch is available free of charge for non-commercial research institutions.