GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses.

Q2 Decision Sciences

Source Code for Biology and Medicine Pub Date : 2013-08-29 DOI:10.1186/1751-0473-8-17

Hidetoshi Itaya, Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita

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引用次数: 12

Abstract

The popular European Molecular Biology Open Software Suite (EMBOSS) currently contains over 400 tools used in various bioinformatics researches, equipped with sophisticated development frameworks for interoperability and tool discoverability as well as rich documentations and various user interfaces. In order to further strengthen EMBOSS in the fields of genomics, we here present a novel EMBOSS associated software (EMBASSY) package named GEMBASSY, which adds more than 50 analysis tools from the G-language Genome Analysis Environment and its Representational State Transfer (REST) and SOAP web services. GEMBASSY basically contains wrapper programs of G-language REST/SOAP web services to provide intuitive and easy access to various annotations within complete genome flatfiles, as well as tools for analyzing nucleic composition, calculating codon usage, and visualizing genomic information. For example, analysis methods such as for calculating distance between sequences by genomic signatures and for predicting gene expression levels from codon usage bias are effective in the interpretation of meta-genomic and meta-transcriptomic data. GEMBASSY tools can be used seamlessly with other EMBOSS tools and UNIX command line tools. The source code written in C is available from GitHub (https://github.com/celery-kotone/GEMBASSY/) and the distribution package is freely available from the GEMBASSY web site (http://www.g-language.org/gembassy/).

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GEMBASSY: EMBOSS相关软件包，用于全面的基因组分析。

流行的欧洲分子生物学开放软件套件(EMBOSS)目前包含400多个用于各种生物信息学研究的工具，配备了复杂的开发框架，用于互操作性和工具可发现性，以及丰富的文档和各种用户界面。为了进一步加强EMBOSS在基因组学领域的应用，我们提出了一种新的EMBOSS关联软件(EMBASSY)包GEMBASSY，它增加了来自g语言基因组分析环境及其Representational State Transfer (REST)和SOAP web服务的50多个分析工具。GEMBASSY主要包含g语言REST/SOAP web服务的包装程序，以提供对完整基因组平面文件中各种注释的直观和方便的访问，以及分析核酸组成、计算密码子使用和可视化基因组信息的工具。例如，通过基因组特征计算序列之间的距离和通过密码子使用偏差预测基因表达水平等分析方法在解释元基因组和元转录组数据方面是有效的。GEMBASSY工具可以与其他EMBOSS工具和UNIX命令行工具无缝使用。用C编写的源代码可以从GitHub (https://github.com/celery-kotone/GEMBASSY/)获得，发行包可以从GEMBASSY网站(http://www.g-language.org/gembassy/)免费获得。

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来源期刊

Source Code for Biology and Medicine Decision Sciences-Information Systems and Management

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期刊介绍： Source Code for Biology and Medicine is a peer-reviewed open access, online journal that publishes articles on source code employed over a wide range of applications in biology and medicine. The journal"s aim is to publish source code for distribution and use in the public domain in order to advance biological and medical research. Through this dissemination, it may be possible to shorten the time required for solving certain computational problems for which there is limited source code availability or resources.