Computer Science Department, University of Missouri, Columbia, MO 65211, USA.
BMC Plant Biol. 2010 Jan 18;10:14. doi: 10.1186/1471-2229-10-14.
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/.
转录因子在调节基因表达方面起着至关重要的作用，几乎影响着所有的生物过程。系统地识别和注释转录因子可以极大地帮助我们进一步了解它们的功能和机制。在本文中，我们介绍了 SoyDB，这是一个用户友好的数据库，包含了大豆转录因子的综合知识。
大豆基因组最近由能源部-联合基因组研究所（DOE-JGI）测序，并公开可用。对该序列的挖掘鉴定出了 5671 个大豆基因作为潜在的转录因子。这些基因被全面注释，以帮助大豆研究界。我们开发了 SoyDB——一个大豆基因组中所有转录因子的知识库。该数据库包含蛋白质序列、预测的三级结构、假定的 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、一致的蛋白质序列基序、每个家族的 Web 标志和大豆转录因子数据库 PlantTFDB、已知 EST 序列以及其他一般蛋白质数据库（包括 Swiss-Prot、Gene Ontology、KEGG、EMBL、TAIR、InterPro、SMART、PROSITE、NCBI 和 Pfam）的网络链接。该数据库可通过交互式和方便的 Web 服务器访问，支持全文搜索、PSI-BLAST 序列搜索、按蛋白质家族浏览数据库以及通过隐马尔可夫模型自动将新蛋白质序列分类为 64 个注释转录因子家族之一。
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/ 上公开提供。
