PreDetector : Prokaryotic Regulatory Element Detector

PreDetector is a stand-alone software, written in java. Its final aim is to predict regulatory sites for prokaryotic species. It comprises two functionalities.
The first one is very similar to Target Explorer1. From a set of sequences identified as potential target sites, PreDetector creates a consensus sequence and computes its scoring matrix. This sequence and matrix can be saved on a file and, then, be used to find along a selected genome the sequences that are close enough to the consensus sequence. To this end, a score is attributed to each locus in the genome according to the similarity measure defined by the matrix. The output of this functionality is filtered with a cut-off score and then directly used as input by the second one.
The second functionality starts by fetching the gene positions of the selected species from the NCBI server. The loci having above cut-off score are then classified into four classes, allowing multiple classes for one element. This gives the biologists a better view of his discovered sequences.