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Updated: Jul 17, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
Published on: February 7, 2019
Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences
Abstract:
This paper describes a novel approach to constructing position-specific weight matrices (PWM) based on the transcription factor binding site (TFBS) data provide by the TRANSFAC database, and the comparison of the thus generated PWMs with the original TRANSFAC matrices. Multiple local sequence alignment was performed on the TFBSs of each transcription factor. Several different alignment programs were tested and their matrices were compared to the original TRANSFAC matrices. One of the alignment programs, GLAM, produced comparable matrices in terms of the average ranking of true positive sites across the whole test set of sequences.
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