Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology
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DOI：
10.1093/bib/bbv079
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发表时间：
2016-09-01
影响因子：
9.5
通讯作者：
Caspi, Ron
中科院分区：
文献类型：
--
作者：
Karp, Peter D.;Latendresse, Mario;Caspi, Ron
Pathway Tools 是一个具有广泛功能的生物信息学软件环境。该软件提供基因组信息学工具，例如基因组浏览器、序列比对、基因组变异分析器和比较基因组学操作。它提供代谢信息学工具，例如代谢重建、定量代谢建模、反应原子映射预测和代谢途径搜索。 Pathway Tools 还提供监管信息学工具，例如表示和可视化各种监管交互的能力。本文概述了过去 5 年中 Pathway Tools 的进展。主要新增内容包括代谢建模、代谢途径搜索、原子映射计算和化合物吉布斯形成自由能估计组件；添加信号通路、基因组序列和细胞结构的编辑器；基因必要性数据和表型数据的存储；显示多重排列、信号传导和电子传输途径； Python 和网络服务应用程序编程接口的开发。世界各地的科学家使用 Pathway Tools 创建了超过 9800 个路径/基因组数据库，其中许多是重要模式生物的精选数据库。
Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms.