Abstract
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. XFITOM IS AVAILABLE FOR DOWNLOAD AT: http://research.umbc.edu/˜erill.
Highlights
The discovery and analysis of transcriptional regulatory networks is a key step in elucidating the complex regulatory apparatus of living beings [1]
Site search algorithms take in a motif description and use pattern matching techniques to search for sites on DNA sequences [4]
Methods based on based on regular expression syntaxes use IUPAC codes for degenerate bases and allow for complex motif descriptions including gaps, multiple repeats and variable spacers [3]
Summary
The discovery and analysis of transcriptional regulatory networks is a key step in elucidating the complex regulatory apparatus of living beings [1]. The semi-specific recognition of binding sites by their cognate transcription factors allows implementing computational tools for the discovery and detection of transcription binding motifs and sites [1]. Site search algorithms take in a motif description and use pattern matching techniques to search for sites on DNA sequences [4]. Scanning genomic sequences leads to a noisy but informative reconstruction of transcriptional regulatory networks, which can be later validated by in vitro and in vivo methods [5].
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