Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.
Plastid: nucleotide-resolution analysis of next-generation sequencing and genomics data.
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DOI：
10.1186/s12864-016-3278-x
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发表时间：
2016-11-22
期刊：
影响因子：
4.4
通讯作者：
Weissman JS
中科院分区：
文献类型：
--
作者：
Dunn JG;Weissman JS
下一代测序(NGS)以前所未有的深度和核苷酸分辨率揭示了许多生物学问题。这些分析产生了对分析工具的需求，使用户能够有力而轻松地逐个核苷酸地处理数据。此外，由于许多NGS分析在读取比对的多种性质内联合编码信息--例如，在核糖体分析中，核糖体的位置在比对坐标中联合编码，并且在分析之前通常需要长度分析工具来从比对中提取生物学意义。为此目的，存在许多分析专用管道，但仍然需要用户友好的、通用的、不限于特定实验制度或分析工作流程的核苷酸解析工具。Plattid是一种专为基因组和NGS数据的核苷酸解析分析而设计的巨蟒文库。因此，plettid被设计用来从读取比对中提取分析特异性信息，同时保持对新的NGS分析的通用性和可扩展性。Plattid将NGS和其他生物数据表示为与基因组或转录位置相关的值阵列，并包含可配置的工具，用于将来自各种来源的数据转换为此类阵列。Plattid还包括许多工具，可以精确地操纵不连续的基因组特征，如剪接的转录本。Plattid自动处理基因组坐标和以特征为中心的坐标之间的转换，考虑到剪接和链，将用户从繁琐的计算中解放出来。最后，Plattid的数据模型使用一致和熟悉的生物学习语，即使是初学者也能以最少的努力开发复杂的分析工作流程。Plattid是一个多用途的工具包，已被用于分析来自多种NGS分析的数据，包括RNA-seq、核糖体图谱和DMS-seq。它构成了我们的ORF注释工具ORF-Rater的基因组引擎，并很容易适应新的NGS分析。有关示例、教程和大量文档，请访问https://plastid.readthedocs.io.
Next-generation sequencing (NGS) informs many biological questions with unprecedented depth and nucleotide resolution. These assays have created a need for analytical tools that enable users to manipulate data nucleotide-by-nucleotide robustly and easily. Furthermore, because many NGS assays encode information jointly within multiple properties of read alignments ― for example, in ribosome profiling, the locations of ribosomes are jointly encoded in alignment coordinates and length ― analytical tools are often required to extract the biological meaning from the alignments before analysis. Many assay-specific pipelines exist for this purpose, but there remains a need for user-friendly, generalized, nucleotide-resolution tools that are not limited to specific experimental regimes or analytical workflows. Plastid is a Python library designed specifically for nucleotide-resolution analysis of genomics and NGS data. As such, Plastid is designed to extract assay-specific information from read alignments while retaining generality and extensibility to novel NGS assays. Plastid represents NGS and other biological data as arrays of values associated with genomic or transcriptomic positions, and contains configurable tools to convert data from a variety of sources to such arrays. Plastid also includes numerous tools to manipulate even discontinuous genomic features, such as spliced transcripts, with nucleotide precision. Plastid automatically handles conversion between genomic and feature-centric coordinates, accounting for splicing and strand, freeing users of burdensome accounting. Finally, Plastid’s data models use consistent and familiar biological idioms, enabling even beginners to develop sophisticated analytical workflows with minimal effort. Plastid is a versatile toolkit that has been used to analyze data from multiple NGS assays, including RNA-seq, ribosome profiling, and DMS-seq. It forms the genomic engine of our ORF annotation tool, ORF-RATER, and is readily adapted to novel NGS assays. Examples, tutorials, and extensive documentation can be found at https://plastid.readthedocs.io.
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核糖体分析揭示了果蝇果蝇中普遍存在的终止密码子读取。
影响因子：
7.7
作者：
Dunn JG;Foo CK;Belletier NG;Gavis ER;Weissman JS
通讯作者：
Weissman JS
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
影响因子：
56.9
作者：
Kryukov, GV;Castellano, S;Gladyshev, VN
通讯作者：
Gladyshev, VN
DOI：
10.1126/science.1257521
发表时间：
2014-11-07
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Jan CH;Williams CC;Weissman JS
通讯作者：
Weissman JS