ems2

Improved algorithms for findinding edit distance based motifs

Usage: ./ems [OPTIONS] <input-sequence-file>
	-s <version>  Possible versions: 1, 2, 2m, 2p
	-l <l>        Length (l) of (l,d) motif
	-d <d>        Maximum edit distance (d) of (l,d) motif
	-t <int>      Number of threads

The option -t is applicable to version 2p only. Other versions are single threaded.

Build

$ cd src
$ make

Run

$ cd src
$ ems -s 2p -l 16 -d 3 -t 8 ../test/planted_l16_d3.txt

References

• Soumitra Pal, Sanguthevar Rajasekaran, "Improved algorithms for finding edit distance based motifs", IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 2015, pp. 537-542, doi:10.1109/BIBM.2015.7359740