Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.
Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database.
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DOI：
10.1093/bioinformatics/btn529
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发表时间：
2008-12-01
期刊：
影响因子：
--
通讯作者：
Rajandream MA
中科院分区：
文献类型：
--
作者：
Carver T;Berriman M;Tivey A;Patel C;Böhme U;Barrell BG;Parkhill J;Rajandream MA
动机：阿耳特弥斯（Artemis）和阿耳特弥斯比较工具（ACT）已成为查看和注释序列数据的主流工具，尤其适用于微生物基因组。自首次发布以来，阿耳特弥斯一直在持续开发，并根据实验室生物学家和专业注释人员等活跃用户群体的反馈，增加了用于编辑和分析序列的功能。然而，它只能从平面文件进行读写的局限性在一定程度上限制了其实用性。因此，开发了一个新版本的阿耳特弥斯，它可以对关系数据库模式进行读写，并允许用户注释更复杂（通常是庞大且碎片化的）基因组序列。
结果：阿耳特弥斯和ACT现已扩展为可直接对通用模式生物数据库（GMOD，http://www.gmod.org）的Chado关系数据库模式进行读写。此外，还开发了一个基因构建工具，用于提供结构化的表单和表格，以根据标准本体、受控词汇表和自由文本编辑基因模型的坐标以及编辑功能注释。
可用性：阿耳特弥斯和ACT可在威康桑格研究所网站（http://www.sanger.ac.uk/Software/Artemis/ ，http://www.sanger.ac.uk/Software/ACT/）上免费下载（适用于MacOSX、UNIX和Windows，遵循GPL许可）。
联系方式：artemis@sanger.ac.uk
补充信息：补充数据可在《生物信息学》在线网站获取。
Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
14.9
作者：
Mulder NJ;Apweiler R;Attwood TK;Bairoch A;Bateman A;Binns D;Bork P;Buillard V;Cerutti L;Copley R;Courcelle E;Das U;Daugherty L;Dibley M;Finn R;Fleischmann W;Gough J;Haft D;Hulo N;Hunter S;Kahn D;Kanapin A;Kejariwal A;Labarga A;Langendijk-Genevaux PS;Lonsdale D;Lopez R;Letunic I;Madera M;Maslen J;McAnulla C;McDowall J;Mistry J;Mitchell A;Nikolskaya AN;Orchard S;Orengo C;Petryszak R;Selengut JD;Sigrist CJ;Thomas PD;Valentin F;Wilson D;Wu CH;Yeats C
通讯作者：
Yeats C
影响因子：
5.8
作者：
Carver, TJ;Rutherford, KM;Parkhill, J
通讯作者：
Parkhill, J
影响因子：
9.5
作者：
Berriman, Matt;Rutherford, Kim
通讯作者：
Rutherford, Kim
影响因子：
5.6
作者：
Bendtsen, JD;Nielsen, H;Brunak, S
通讯作者：
Brunak, S
影响因子：
5.8
作者：
Rutherford, K;Parkhill, J;Barrell, B
通讯作者：
Barrell, B