Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences.
Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences.
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DOI：
10.1093/nar/gkaa1052
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发表时间：
2021-01-11
影响因子：
14.9
通讯作者：
Ahituv N
中科院分区：
文献类型：
--
作者：
Georgakopoulos-Soares I;Mouratidis I;Parada GE;Matharu N;Hemberg M;Ahituv N
DNA链的不对称性可以对几种生物学功能产生重大影响，包括复制、转录和转录因子结合。因此，DNA链不对称性和突变链偏好可以提供有关生物功能的信息。然而，探索这一点的通用工具并不存在。在这里，我们提出了一个用户友好的计算工具，进行统计分析和可视化的链不对称性的评估。Aprion将提供有链注释的DNA特征作为输入，并输出单个DNA特征或特征对之间连续出现的链不对称性。我们说明了使用的Aesthion通过确定转录和复制链的不对称性的种系结构变异的断点。我们还表明，分析的45%的人类转录因子的结合位点的方向在转录区域具有显著的DNA链偏好，这也在ChIP-seq分析中得到证实，并且可能与转录相关。总之，我们提供了一种新的工具来评估DNA链的不对称性，并展示了如何使用它来获得跨各种生物学科的新见解。
DNA strand asymmetries can have a major effect on several biological functions, including replication, transcription and transcription factor binding. As such, DNA strand asymmetries and mutational strand bias can provide information about biological function. However, a versatile tool to explore this does not exist. Here, we present Asymmetron, a user-friendly computational tool that performs statistical analysis and visualizations for the evaluation of strand asymmetries. Asymmetron takes as input DNA features provided with strand annotation and outputs strand asymmetries for consecutive occurrences of a single DNA feature or between pairs of features. We illustrate the use of Asymmetron by identifying transcriptional and replicative strand asymmetries of germline structural variant breakpoints. We also show that the orientation of the binding sites of 45% of human transcription factors analyzed have a significant DNA strand bias in transcribed regions, that is also corroborated in ChIP-seq analyses, and is likely associated with transcription. In summary, we provide a novel tool to assess DNA strand asymmetries and show how it can be used to derive new insights across a variety of biological disciplines.
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DOI：
10.1261/rna.048280.114
发表时间：
2016-02
期刊：
RNA (New York, N.Y.)
影响因子：
--
作者：
Kim EZ;Wespiser AR;Caffrey DR
通讯作者：
Caffrey DR
DOI：
10.1093/bioinformatics/btr064
发表时间：
2011-04-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Grant CE;Bailey TL;Noble WS
通讯作者：
Noble WS
影响因子：
14.9
作者：
Frankish A;Diekhans M;Ferreira AM;Johnson R;Jungreis I;Loveland J;Mudge JM;Sisu C;Wright J;Armstrong J;Barnes I;Berry A;Bignell A;Carbonell Sala S;Chrast J;Cunningham F;Di Domenico T;Donaldson S;Fiddes IT;García Girón C;Gonzalez JM;Grego T;Hardy M;Hourlier T;Hunt T;Izuogu OG;Lagarde J;Martin FJ;Martínez L;Mohanan S;Muir P;Navarro FCP;Parker A;Pei B;Pozo F;Ruffier M;Schmitt BM;Stapleton E;Suner MM;Sycheva I;Uszczynska-Ratajczak B;Xu J;Yates A;Zerbino D;Zhang Y;Aken B;Choudhary JS;Gerstein M;Guigó R;Hubbard TJP;Kellis M;Paten B;Reymond A;Tress ML;Flicek P
通讯作者：
Flicek P
影响因子：
64.5
作者：
Haradhvala NJ;Polak P;Stojanov P;Covington KR;Shinbrot E;Hess JM;Rheinbay E;Kim J;Maruvka YE;Braunstein LZ;Kamburov A;Hanawalt PC;Wheeler DA;Koren A;Lawrence MS;Getz G
通讯作者：
Getz G
影响因子：
4.4
作者：
Inoue F;Ahituv N
通讯作者：
Ahituv N