TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites

作     者：Umair Seemab Qurrat ul Ain Muhammad Sulaman Nawaz Zafar Saeed Sajid Rashid 

作者机构：National Centre for Bioinformatics Quaid-i-Azam University Department of Computer Science Quaid-i-Azam University 

出 版 物：《Genomics, Proteomics & Bioinformatics》 (基因组蛋白质组与生物信息学报（英文版）)

年 卷 期：2012年第10卷第6期

页      面：354-359页

核心收录：

学科分类：0710[理学-生物学] 07[理学] 071007[理学-遗传学] 

基　　金：supported by Higher Education Commission  Pakistan(Grant No.20-1493/R&D/09) 

主　　题：TrFAST Transcription factor binding sites in silico analysis Signaling pathway Pattern searching 

摘      要：Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mech- anisms underlying normal and dysfunctional biological processes. Here we present a novel computational tool, transcription factor search and analysis tool （TrFAST）, which was developed for the in silico analysis of transcription factor binding sites （TFBSs） of sig- naling pathway-specific TFs. TrFAST facilitates searching as well as comparative analysis of regulatory motifs through an exact pattern matching algorithm followed by the graphical representation of matched binding sites in multiple sequences up to 50 kb in length. TrFAST is proficient in reducing the number of comparisons by the exact pattern matching strategy. In contrast to the pre-existing tools that find TFBS in a single sequence, TrFAST seeks out the desired pattern in multiple sequences simultaneously. It counts the GC con- tent within the given multiple sequence data set and assembles the combinational details of consensus sequence（s） located at these regions, thereby generating a visual display based on the abundance of unique pattern. Comparative regulatory region analysis of multi- ple orthologous sequences simultaneously enhances the features of TrFAST and provides a significant insight into study of conservation of non-coding cis-regulatory elements. TrFAST is freely available at http：//***/***.