The MREC download page can be accessed at Project Homepage.
MREC is a new computational method for solving a classical problem, the identification problem of cis regulatory motifs in a given set of promoter sequences, based on one key new idea. Instead of scoring candidate motifs individually like in all the existing motif finding programs, our method scores groups of candidate motifs with similar sequences, called motif closures, using a p-value, which substantially improved the prediction reliability over the existing methods. Our new p-value scoring scheme is sequence length indepe ndent, hence allowing direct comparisons among predicted motifs with different lengths on the same footing. We have implemented this method as a computer program MREC, and have extensively tested MREC on both simulated and biological data from prokaryotic genomes. Our test results indicate that MREC can accurat ely pick out the actual motif with the correct length as the best scoring candidate for the vast majority of the cases in our test set. We compared our prediction results with two motif finding programs Cosmo and MEME, and found that MREC substantially outperforms both programs across all the test cases, illustrating the major progress in our ability to find cis regulatory motifs represented by the development of MREC. One more important feature is that the MREC program is essentially able to extract all the actual motifs by outputting multiple best candidate motifs if the test sequence data does have that many.
Note
MREC currently will only run on linux platform, as it is dependent on GNU function.
Simply put “MREC1.0.tar.gz” in any directory:
$ tar -xvf MREC1.0.tar.gz
enter the folder MREC1.0 and type ./makefile.
There is a shell script named MREC in the provided package. See help and look at all available options, please type:
$ ./MREC
Take a look at input first. If you try to run MREC on a sequences set with fasta format, please type:
$ ./MREC [dataname] {options}
There is a detailed explenation in the file README in the folder MREC1.0. Note that the input data should in the same directory with the shell script MREC.
If you want to run MREC with defaut parameters, please just type:
$ ./MREC [dataname]
If you run MREC in this way, the result can be found in file motif_[dataname].txt in same directory. Or you can provide the result file name with option -o.
Any questions, problems, bugs are welcome and should be dumped to
Bingqiang Liu<bingqiang@csbl.bmb.uga.edu>