soydb a knowledge database of soybean transcription factorssoydb大豆转录因子的知识数据库.pdfVIP

Wang et al. BMC Plant Biology 2010, 10:14 /1471-2229/10/14 DATABASE Open Access SoyDB: a knowledge database of soybean transcription factors 1 2,3 1,2 2,3 2,3 1,2,4 2,3 Zheng Wang , Marc Libault , Trupti Joshi , Babu Valliyodan , Henry T Nguyen , Dong Xu , Gary Stacey , Jianlin Cheng1,2,4* Abstract Background: 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. Description: 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 we