Romeuf et al. BMC Genomics 2010, 11:185 http://www.biomedcentral.com/1471-2164/11/185 Page 3 of 15 Figure 1 Schematic representation of the wDBTF wheat transcription factor database. The core database contains rice gene models from DRTF. The wheat data is made up of publicly available expressed sequences either singletons or assembled contigs. wDBTF includes information on 7,112 identified wheat TFs, on the DNA-binding domains (where known) and on in silico expression. Only the protein sequence regions that matched a TF sequence were taken into account. The presence of DNA-binding domain for each wheat TF sequence iden- tified was searched against the Pfam database. The e- value cut-off 1e-01 was used in the initial Hidden Mar- kov Model (HMMer) searches. For families which have no DNA-binding domain profiles available in the Pfam database, each sequence was analyzed individually to decide the cut-off value and sequences with more than 60% identity with their respective sequences from rice were considered to be bona fide members. The Affymetrix wheat genome array contains 61,127 probe sets which represent 55,052 transcripts. Blast searches were performed against the probe set data to assign an Affymetrix ID to individual sequences. Details of the all the original EST libraries were col- lated from the NCBI Unigene site http://www.ncbi.nlm. nih.gov/unigene. The list of 226 libraries used for this database is provided in Additional file 1. The origins of expressed sequences were classified in six categories: root, crown, shoot, leaf, whole plant if the origin is unknown, and spike for whole organs and tissues within the spike at different developmental stages from flower- ing to maturation (Figure 2). All data were imported and formatted using custom PERL scripts and stored in a PostgreSQL database, named wDBTF, publicly available at http://wwwappli. nantes.inra.fr:8180/wDBFT/. The web site was developed with Java applet and servlet technologies. The wDBTF web pages are conceptual views of the PostgreSQL rela- tional database. Identification of TFs in T. aestivum Comparative analysis of wheat and rice TFs based on sequence identity was performed to identify all unique TFs in public transcript sequences of wheat. Each of the 216,452 unique wheat sequences (contigs and singletons) from the TIGR assembly of ESTs and transcripts was systematically compared with rice TF proteins using Blastx. The sequences matching rice TFs (e-value < 1e-05) were defined as TF-encoding sequences. Any sequences which did not correspond to potential TFs were discarded. In this way we found 7,112 accessions from TIGR correspond to T. aestivum TFs. These sequences were represented by 3,790 TCs and 3,322 singletons (Table 1). Evidence of a conserved DNA-binding domain was detected for 51.8% of the wheat sequences identified, i.e. 3,681 sequences (Table 1). For 8 (GRF, LUG, NZZ, Trihelix, ULT, Whirly, HRT-like and VOZ) out of 84 subfamilies, no DNA- binding domain motifs are available in the Pfam data- base, so we established whether a wheat sequence