DNA shape complements sequence-based representations of transcription factor binding sites

Author:

DeFord PeterORCID,Taylor JamesORCID

Abstract

AbstractThe position weight matrix (PWM) has long been a useful tool for describing variation in the composition of regions of DNA such as transcription factor (TF) binding sites. It is difficult, however, to relate the sequence-based representation of a DNA motif to the biological features of the interaction of a TF with its binding site. Here we present an alternative strategy for representing DNA motifs – called Structural Motif (StruM) – that can easily represent different sets of structural features. Structural features are inferred from dinucleotide properties listed in the Dinucleotide Property Database. StruMs are able to specifically model TF binding sites, using an encoding strategy that is distinct from sequence-based models. This difference in encoding strategies makes StruMs complementary to sequence-based methods of TF binding site identification.

Publisher

Cold Spring Harbor Laboratory

Reference34 articles.

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3