/motifSearch

Snow's motif search

Primary LanguageC

motifSearch

Current version: 0.0.2 == multi-threaded searching

Snow's motif search in C (A simple command-line-tool, expecting to be faster than homer's scanMotifGenome)

Motif searching supporting IUPAC ambiguous codes.

Usage

motifSearch -f <FASTA> -m <MOTIF> -p <THREAD> > <OUTPUT-BED>
-f/--fasta      fasta file
-m/--motif      motif string
-p/--nthreads   number of threads

To compile, make && make clean

TODO

  • stats compare to other methods
  • mismatch handling