利用转录因子结合位点序列的多重局部比对改进TRANSFAC矩阵。

Improvement of TRANSFAC matrices using multiple local alignment of transcription factor binding site sequences.

作者信息

Fu Yutao, Weng Zhiping

机构信息

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

出版信息

Genome Inform. 2005;16(1):68-72.

PMID:16362908

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.

摘要

本文描述了一种基于TRANSFAC数据库提供的转录因子结合位点（TFBS）数据构建位置特异性权重矩阵（PWM）的新方法，并将新生成的PWM与原始TRANSFAC矩阵进行比较。对每个转录因子的TFBS进行了多序列局部比对。测试了几种不同的比对程序，并将它们的矩阵与原始TRANSFAC矩阵进行比较。其中一个比对程序GLAM，就整个测试序列集上真实阳性位点的平均排名而言，产生了可比的矩阵。