Title

xFITOM: a generic GUI tool to search for transcription factor binding sites

Authors

Nidhi Bhargava, Ivan Erill*

Affiliation

Department of Biological Sciences, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA

E-mail*

erill@umbc.edu; * Corresponding author

Article Type

Hypothesis

Date

received  May 27, 2010; accepted  June29, 2010; published July 6, 2010

Locating transcription factor binding sites in genomic sequences is a key step in deciphering transcription networks. Currently available software for site search is mostly server-based, limiting the range and flexibility of this type of analysis. xFITOM is a fully customizable program for locating binding sites in genomic sequences written in C++. Through an easy-to-use interface, xFITOM that allows users an unprecedented degree of flexibility in site search. Among other features, it enables users to define motifs by mixing real sites and IUPAC consensus sequences, to search the annotated sequences of unfinished genomes and to choose among 11 different search algorithms. 

Availability

Keywords

Transcription factor, binding site, site search, motif prediction, genome analysis

Citation

Erill et al. Bioinformation 5(2): 49-51 (2010)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.