SeqHound: biological sequence and structure database as a platform for bioinformatics research.
SeqHound: biological sequence and structure database as a platform for bioinformatics research.
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DOI：
10.1186/1471-2105-3-32
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发表时间：
2002-10-25
影响因子：
3
通讯作者：
Hogue CW
中科院分区：
文献类型：
--
作者：
Michalickova K;Bader GD;Dumontier M;Lieu H;Betel D;Isserlin R;Hogue CW
SeqHound是一个集成了生物序列、分类学、注释和三维结构数据库的系统。它为本地托管环境中的生物信息学研究提供了高性能服务器平台。SeqHound是基于国家生物技术信息中心的数据模型和编程工具。它提供每日更新的内容，除了3-D结构数据和有关序列冗余，序列邻居，分类学，完整基因组，功能注释（包括基因本体论术语和PubMed文献链接）的信息外，还提供了所有DALZ序列数据库的内容。SeqHound可通过Perl、C或C++远程API或优化的本地API通过Web服务器访问。它提供检索序列、结构和结构域的专门子集所需的功能。可以FASTA、GenBank、ASN. 1和XML格式检索序列。结构有ASN.1、XML和PDB格式。重点放在完整的基因组，分类，域和功能注释以及三维结构功能的API，而外地文本索引功能仍在开发中。SeqHound还提供了一个简化的WWW界面，用于简单的Web用户查询。该系统已被证明是有用的几个已发表的生物信息学项目，如BIND数据库，并提供了一个具有成本效益的基础设施的研究。SeqHound将继续开发，并作为Samuel Lunenfeld研究所蓝图计划的一项服务提供。源代码和示例可以在Sourceforge网站http://sourceforge.net/projects/slritools/的SLRI工具包中根据GNU公共许可证的条款获得。
SeqHound has been developed as an integrated biological sequence, taxonomy, annotation and 3-D structure database system. It provides a high-performance server platform for bioinformatics research in a locally-hosted environment. SeqHound is based on the National Center for Biotechnology Information data model and programming tools. It offers daily updated contents of all Entrez sequence databases in addition to 3-D structural data and information about sequence redundancies, sequence neighbours, taxonomy, complete genomes, functional annotation including Gene Ontology terms and literature links to PubMed. SeqHound is accessible via a web server through a Perl, C or C++ remote API or an optimized local API. It provides functionality necessary to retrieve specialized subsets of sequences, structures and structural domains. Sequences may be retrieved in FASTA, GenBank, ASN.1 and XML formats. Structures are available in ASN.1, XML and PDB formats. Emphasis has been placed on complete genomes, taxonomy, domain and functional annotation as well as 3-D structural functionality in the API, while fielded text indexing functionality remains under development. SeqHound also offers a streamlined WWW interface for simple web-user queries. The system has proven useful in several published bioinformatics projects such as the BIND database and offers a cost-effective infrastructure for research. SeqHound will continue to develop and be provided as a service of the Blueprint Initiative at the Samuel Lunenfeld Research Institute. The source code and examples are available under the terms of the GNU public license at the Sourceforge site http://sourceforge.net/projects/slritools/ in the SLRI Toolkit.
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