Genome Informatics
Online ISSN : 2185-842X
Print ISSN : 0919-9454
ISSN-L : 0919-9454
Improvement of TRANSFAC Matrices Using Multiple Local Alignment of Transcription Factor Binding Site Sequences
Yutao FuZhiping Weng
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Keywords: GLAM, TRANSFAC, matrix
JOURNAL FREE ACCESS

2005 Volume 16 Issue 1 Pages 68-72

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Abstract

This paper describes a novel approach to constructing Position-Specific Weight Matrices (PWMs) based on the transcription factor binding site (TFBS) data provide by the TRANSFAC database and comparison of the newly 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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© Japanese Society for Bioinformatics
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