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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
Published on: February 7, 2019
A novel approach for transcription factor analysis using SELEX with high-throughput sequencing (TFAST)
Daniel J Reiss1, Frederick M Howard, Harry L T Mobley
1Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, United States of America.
Plos One
|September 8, 2012
Summary
TFAST software accurately identifies transcription factor binding sites using aptamer-free SELEX-seq data. This intuitive tool rapidly analyzes data, predicting binding site length and motif, aiding in understanding protein-DNA interactions.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Developed modified aptamer-free SELEX-seq (afSELEX-seq) for transcription factor binding site discovery.
- Introduced TFAST, novel software for analyzing afSELEX-seq data.
- TFAST features a user-friendly Java interface for accessibility.
Purpose of the Study:
- To present and validate the TFAST software for afSELEX-seq data analysis.
- To demonstrate TFAST's capability in identifying and characterizing transcription factor binding sites.
- To provide an efficient and accurate tool for bioinformatics analysis.
Main Methods:
- TFAST aligns afSELEX-seq data to a reference genome.
- It identifies and compares peak characteristics across experimental cycles.
- Generates hierarchical reports with peak data, genomic sequences, and motif predictions.
Main Results:
- Increased afSELEX-seq cycles enhanced peak identification accuracy.
- TFAST identified 457 strong candidate binding sites from 7,274 initial peaks.
- Analysis revealed increasing motif significance and informational content in top-ranked peaks.
- Predicted binding site length (28 bp) aligned with experimental data for PapX.
Conclusions:
- TFAST provides an intuitive and novel method for afSELEX-seq data analysis.
- The software accurately predicts transcription factor binding site length and motif.
- TFAST enables rapid and precise identification of DNA-protein interactions.
