Skip to Main Content



Multi-platform GUI-enabled standalone software for detection of binding sites in genetic sequences

jFITOM is a Java version of FITOM. Like xFITOM, jFITOM uses a set of aligned sites and/or IUB consensus sequences to construct a position-specific frequency matrix and search a set sequences for putative binding sites. It can be donwloaded or run as an applet and provides fast searches for annotated genomes. Among other improvements, jFITOM returns relevant annotation on both genomic strands and operon information.

Donwload jFITOM (jar file)

User manual (PDF)

Run jFITOM as an applet

jFITOM library source code (rar file)

jFITOM GUI source code (rar file)

jFITOM requires BioJava


You will need the Java Runtime Environment in order to run jFITOM. To install, jFITOM just donwload the jfitom-run.jar file, save it in the folder of your preference and double click on it to launch jFITOM.


If using xFITOM or jFITOM for your research, please cite:

Bhargava, N. & Erill, I. (2010) “xFITOM: a generic GUI tool to search for transcription factor binding sites”, Bioinformation 5(2) 49-51 [PubMed]