Below are several useful software packages developed in the lab. Feel use to use them and please cite accordingly.
Software
FITOM is a computer program written in C++ for the detection of binding sites in DNA or RNA sequences. It implements several methods described in the literature to compute an approximation of binding affinity for a particular site based on a collection of binding sequences provided by the user. Using this method, FITOM scans a sequence file looking for putative binding sites across the DNA/RNA sequence in both strands, and filters the results according to a user-specified threshold. If sequence annotation is provided in the sequence file, FITOM will also link the identified sites with annotated genes and it will infer their role from their location in the vicinity of genes.