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

xFITOM is a fully featured GUI-enabled version of FITOM for Ms-Windows platforms that integrates additional functionality. The program provides an easy to use graphical user interface (GUI) to define all the relevant options for locating binding sites in genetic sequences. xFITOM will scan DNA or RNA sequences looking for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format or a combination of the two. xFITOM implements 11 different detection methods based on information theory as applied to the modeling of binding motifs. It also can take into account local complexity factors such as local motif enrichment. The new GUI-enabled version also allows to integrate multiple GenBank sequences into a single GenBank file for direct analysis of newly released genomic data. GenBank annotation, if available, is used to annotate the putative function of located binding sites.

Downloads

Download xFITOM (XP executable, RAR file)

Download xFITOM user manual (PDF)

Installation

To install, just uncompress the provided RAR file into the folder from which you want xFITOM to operate and double click on the xFITOM.exe application. Several example files and an example guide (ExampleGuide.txt) are also provided in the RAR file.

Citation

If using xFITOM 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]