title: SoyDB: a knowledge database of soybean transcription factors.
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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  A comprehensive soybean transcription factor database was constructed and made publicly accessible at http://casp.rnet.missouri.edu/soydb/.
authors.affiliation: Computer Science Department, University of Missouri, Columbia, MO 65211, USA.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Wang
authors.forename: Marc
authors.initials: M
authors.lastname: Libault
authors.forename: Trupti
authors.initials: T
authors.lastname: Joshi
authors.forename: Babu
authors.initials: B
authors.lastname: Valliyodan
authors.forename: Henry T
authors.initials: HT
authors.lastname: Nguyen
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.forename: Gary
authors.initials: G
authors.lastname: Stacey
authors.forename: Jianlin
authors.initials: J
authors.lastname: Cheng
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D018745:Genome, Plant; D008390:Markov Chains; D010940:Plant Proteins / Q000235:genetics*; D013025:Glycine max / Q000235:genetics*; D014157:Transcription Factors / Q000235:genetics*; D014584:User-Computer Interface
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors