This project includes an efficient parallel algorithm for quorum Planted Motif Search (qPMS). Planted Motif Search (PMS) receives as input n biological sequences and two integers L and D. It returns all possible sequences M of length L such that M occurs in each of the input strings, and each occurrence of M differs from M in no more than D positions. A more practically usable formulation is called quorum PMS (qPMS), which allows the motif to appear in at least q% of the input strings. Therefore, PMS is a special case of qPMS, where q=100%.
This algorithm is described in the following publication
Marius Nicolae & Sanguthevar Rajasekaran, "qPMS9: An Efficient Algorithm for Quorum Planted Motif Search"
See the qpms9 folder for qPMS9 source code and details on how to compile/run.
See the qpms9-data folder for dataset generator source code.
Precompiled Windows binaries
You can find precompiled windows binaries in the examples/win folder. These have been compiled on Windows 7 using MinGW.
Precompiled qpms9 windows executable without parallel execution (no MPI) can be found here.
Please consult the examples/win for sample input/output and scripts to run the programs.
For questions, suggestions, bugs please contact:
Marius Nicolae marius.nicolae (at) engr.uconn.edu