SoyDB: a knowledge database of soybean transcription factors.
SoyDB: a knowledge database of soybean transcription factors.
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DOI：
10.1186/1471-2229-10-14
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发表时间：
2010-01-18
影响因子：
5.3
通讯作者：
Cheng J
中科院分区：
文献类型：
--
作者：
Wang Z;Libault M;Joshi T;Valliyodan B;Nguyen HT;Xu D;Stacey G;Cheng J
转录因子在基因表达调控中起着至关重要的作用，几乎影响着所有的生物学过程。系统地识别和注释转录因子可以极大地帮助进一步理解它们的功能和机制。在这篇文章中，我们提出了一个用户友好的数据库，包含大豆转录因子的全面知识。大豆基因组最近由能源部-联合基因组研究所（DOE-JGI）测序，并公开提供。挖掘这个序列确定了5，671个大豆基因作为假定的转录因子。这些基因被全面注释，以帮助大豆研究界。我们开发了一个包含大豆基因组中所有转录因子的知识数据库。该数据库包含蛋白质序列、预测的三级结构、推定的DNA结合位点、结构域、蛋白质数据库（PDB）中的同源模板、蛋白质家族分类、多序列比对、共有蛋白质序列基序、每个家族的网络徽标以及到大豆转录因子数据库PlantTFDB、已知EST序列和其他通用蛋白质数据库（包括Swiss-Prot、Gene Ontology、KEGG、EMBL、TAIR、InterPro、SMART、PROSITE、NCBI和Pfam。该数据库可以通过一个交互式的和方便的Web服务器，它支持全文检索，PSI-BLAST序列检索，数据库浏览的蛋白质家族，并自动分类的一个新的蛋白质序列到64个注释的转录因子家族的隐马尔可夫模型。构建了一个全面的大豆转录因子数据库，并在http://casp.rnet.missouri.edu/soydb/上公开访问。
Transcription factors play the crucial rule of regulating gene expression and influence almost all biological processes. Systematically identifying and annotating transcription factors can greatly aid further understanding their functions and mechanisms. In this article, we present SoyDB, a user friendly database containing comprehensive knowledge of soybean transcription factors. The soybean genome was recently sequenced by the Department of Energy-Joint Genome Institute (DOE-JGI) and is publicly available. Mining of this sequence identified 5,671 soybean genes as putative transcription factors. These genes were comprehensively annotated as an aid to the soybean research community. We developed SoyDB - a knowledge database for all the transcription factors in the soybean genome. The database contains protein sequences, predicted tertiary structures, putative DNA binding sites, domains, homologous templates in the Protein Data Bank (PDB), protein family classifications, multiple sequence alignments, consensus protein sequence motifs, web logo of each family, and web links to the soybean transcription factor database PlantTFDB, known EST sequences, and other general protein databases including Swiss-Prot, Gene Ontology, KEGG, EMBL, TAIR, InterPro, SMART, PROSITE, NCBI, and Pfam. The database can be accessed via an interactive and convenient web server, which supports full-text search, PSI-BLAST sequence search, database browsing by protein family, and automatic classification of a new protein sequence into one of 64 annotated transcription factor families by hidden Markov models. A comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.
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影响因子：
14.9
作者：
Haft, DH;Loftus, BJ;White, O
通讯作者：
White, O
影响因子：
14.9
作者：
Hubbard, T;Barker, D;Clamp, M
通讯作者：
Clamp, M
影响因子：
14.9
作者：
Corpet, F;Gouzy, J;Kahn, D
通讯作者：
Kahn, D
影响因子：
5.8
作者：
Hwang, Seungwoo;Gou, Zhenkun;Kuznetsov, Igor B.
通讯作者：
Kuznetsov, Igor B.
DOI：
10.1038/80697
发表时间：
2000-11-01
期刊：
NATURE STRUCTURAL BIOLOGY
影响因子：
--
作者：
Burley, SK
通讯作者：
Burley, SK