Detection of binding sites in DNA or RNA sequences

FITOM is a computer program 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.


Download FITOM (XP executable, RAR file)
Download FITOM source code (RAR file)
Download FITOM user manual (PDF)


If using Fitom in your research, please cite either of the following.

  • Abella, M., Campoy, S., Erill, I., Rojo, F., Barbe, J. (2007) “Cohabitation of Two Different lexA Regulons in Pseudomonas putida” J. Bacteriol. 189: 8855-8862 [PubMed]
  • Erill, I; O’Neill, M.C. “A reexamination of information theory-based methods for DNA-binding site identification” BMC Bioinformatics. 2009 Feb 11;10(1):57 [PubMed]