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

Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mechanisms underlying normal and dysfunctional biological processes. Here we present a novel computational tool, transcription factor search and analysis tool (TrFAST), which...

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Autores principales: Seemab, Umair, Ain, Qurrat ul, Nawaz, Muhammad Sulaman, Saeed, Zafar, Rashid, Sajid
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054711/
https://www.ncbi.nlm.nih.gov/pubmed/23317703
http://dx.doi.org/10.1016/j.gpb.2012.06.007
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author Seemab, Umair
Ain, Qurrat ul
Nawaz, Muhammad Sulaman
Saeed, Zafar
Rashid, Sajid
author_facet Seemab, Umair
Ain, Qurrat ul
Nawaz, Muhammad Sulaman
Saeed, Zafar
Rashid, Sajid
author_sort Seemab, Umair
collection PubMed
description Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mechanisms 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 signaling 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 content 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 multiple 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://www.fi-pk.com/trfast.html.
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spelling pubmed-50547112016-10-14 TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites Seemab, Umair Ain, Qurrat ul Nawaz, Muhammad Sulaman Saeed, Zafar Rashid, Sajid Genomics Proteomics Bioinformatics Method Recent advances in the development of high-throughput tools have significantly revolutionized our understanding of molecular mechanisms 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 signaling 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 content 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 multiple 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://www.fi-pk.com/trfast.html. Elsevier 2012-12 2012-12-01 /pmc/articles/PMC5054711/ /pubmed/23317703 http://dx.doi.org/10.1016/j.gpb.2012.06.007 Text en © 2012 Beijing Institute of Genomics, Chinese Academy of Sciences and Genetics Society of China. Published by Elsevier Ltd and Science Press. All rights reserved. http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).
spellingShingle Method
Seemab, Umair
Ain, Qurrat ul
Nawaz, Muhammad Sulaman
Saeed, Zafar
Rashid, Sajid
TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites
title TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites
title_full TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites
title_fullStr TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites
title_full_unstemmed TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites
title_short TrFAST: A Tool to Predict Signaling Pathway-specific Transcription Factor Binding Sites
title_sort trfast: a tool to predict signaling pathway-specific transcription factor binding sites
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054711/
https://www.ncbi.nlm.nih.gov/pubmed/23317703
http://dx.doi.org/10.1016/j.gpb.2012.06.007
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