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An Exploration Into Improving DNA Motif Inference by Looking for Highly Conserved Core Regions

机译：通过寻找高度保守的核心区域探索DNA基序推断的探索

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Although most verified functional elements in noncoding DNA contain a highly conserved core region, this concept is not generally incorporated into de novo motif inference systems. In this work, we explore the utility of adding the notion of conserved core regions into a comparative genomics approach for the search for putative functional elements in noncoding DNA. By modifying the scoring function for GAMI, Genetic Algorithms for Motif Inference, we investigate tradeoffs between the strength of conservation of the full motif vs. the strength of conservation of a core region. This work illustrates that incorporating information about the structure of transcription factor binding sites can be helpful in identifying biologically functional elements.

机译：尽管在非编码DNA中大多数经过验证的功能元件都包含高度保守的核心区域，但通常不会将此概念整合到从头基序推理系统中。在这项工作中，我们探索了将保守核心区域的概念添加到比较基因组学方法中以寻找非编码DNA中假定的功能元件的实用性。通过修改GAMI的计分功能，即“母题推论的遗传算法”，我们研究了完整基序的保守强度与核心区域的保守强度之间的权衡。这项工作表明，纳入有关转录因子结合位点结构的信息可能有助于鉴定生物学功能元件。

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期刊名称 other
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Jeffrey A. Thompson; Clare Bates Congdon;
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年(卷),期 -1(2013),-1
年度 -1
页码 60–67
总页数 22
原文格式 PDF
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专利

1. Intracellular receptor-type transcription factor, LasR, contains a highly conserved amphipathic region which precedes the putative helix—turn—helix DNA binding motif [J] . Jun Fukushima, Kenji Okuda, Minoru Kurata, Nucleic acids research . 1994,第18期

机译：细胞内受体型转录因子LasR包含一个高度保守的两亲性区域，该区域位于推定的螺旋-转-螺旋DNA结合基序之前
2. Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? [J] . Alexandros Bousios, Nikos Darzentas, Athanasios Tsaftaris, BMC Genomics . 2010,第1期

机译：Sirevirus反转录转座子非编码区的高度保守基序：在植物内和植物间分布模式的关键吗？
3. Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants? [J] . Alexandros Bousios, Nikos Darzentas, Athanasios Tsaftaris, BMC Genomics . 2010,第1期

机译：Sirevirus反转录转座子非编码区的高度保守基序：在植物内和植物间分布模式的关键吗？
4. An exploration into improving DNA motif inference by looking for highly conserved core regions [C] . Thompson Jeffrey A., Congdon Clare Bates IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology . 2013

机译：通过寻找高度保守的核心区域来改善DNA基序推理的探索
5. Escherichia coli DNA helicase II: Structure-function analysis of conserved amino acid motifs and investigation of protein-protein interactions [D] . Hall, Mark Christopher. 1998

机译：大肠杆菌DNA解旋酶II：保守氨基酸基序的结构功能分析和蛋白质-蛋白质相互作用的研究
6. The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif [O] . Lina Thoma, Edgardo Sepulveda, Annette Latus, 2014

机译：Lividans链霉菌质粒pIJ101的稳定区编码识别高度保守的短回文序列基序的DNA结合蛋白
7. The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif [O] . Lina eThoma, Edgardo eSepulveda, Annette eLatus, 2014

机译：链霉菌（streptomyces lividans）质粒pIJ101的稳定区编码识别高度保守的短回文序列基序的DNa结合蛋白。

An Exploration Into Improving DNA Motif Inference by Looking for Highly Conserved Core Regions

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