TRANSCRIPTION 14 Current Genomics, 2009, Vol. 10, No. 1 THE DATABASE OF POPLAR FACTORS (DPTF) (CHINA) The Database of Poplar Transcription Factors (DPTF) [12] (http://dptf.cbi.pku.edu.cn/) is dedicated to TFs of the black cottonwood tree poplar (Populus trichocarpa). The homepage gives basic information on the database such as the total (2576) number of TFs gene models, and the number of TF families (64). Strengths of this database are it is con- figured in a way that similar searches can be made against major databases (e.g. UniProt, RefSeq, EMBL, TRANS- FAC) and EST information gathered from numerous mi- croarray [9] experiments are also available to provide the most accurate information about all the putative TFs. Like other databases this database also includes multiple align- ment of DNA-binding domain of each TF family, neighbor- joining phylogenetic tree of each family, and the homolog searches with the Database of Arabidopsis Transcription Factors (DATF). The database can be explored by using the TF family table or by the chromosome table. The putative TF gene models (or putative mRNAs synthesized by the genes) in Populus trichocarpa are included in each table. Under the gene family tab, there is a list of genes organized in a table like manner. The link LinkOut will directly take the viewer to one of the following databases: JGI, DATF, and DRTF. Additionally, like DATF database, other tools like TF gene alignments, phylogenetic tree drawings etc. are available from each TF family page. The page was last up- dated in May 2008. The database is frequently being main- tained and updated. The speed and diligence with which this is done is vital to provide information that will advance the knowledge in the field. The search page gives the viewer the capability to search by database ID (or gene ID) or descrip- tion, by homology relationship (e.g. compare with DATF), and by expression information (e.g. in which plant tissues). The BLAST search allows the user to search a TF amino acid sequences and compare the TF sequences with other plant TF databases like Arabidopsis and rice. THE DATABASE OF TOBACCO TRANSCRIPTION FACTORS (TOBFAC) (USA) The database of tobacco transcription factors (http:// compsysbio.achs.virginia.edu/tobfac/) [13] contains a total of 65 TF families organized in a table like format. The avail- able genes are noted next to the TF family name. The data- base contains a total of over 2513 tobacco TFs. The feature ‘Blast against Tobacco’ consists of selecting what kind of program the viewer is interested in using (blastp, blastn, blastx, tblastn, and tblastx) and what database (Nicotiana tabacum, EST, Genbank, UniGenes, Genbank, and TOBFAC transcription factor sequences) would someone like to use. One can use gene sequence ID, DNA or protein sequence to search for TFs. The ‘EST tobacco Blast’ results generated a total of 572 EST sequences (TOBFAC ID, accession, e- value, definition or information of the EST etc.). The Gen- Bank protein BLAST results in 2354 BLAST outputs, which also have TOBFAC ID, accession, e-value etc. A list of pub- lished papers on each TF family is available under the list of papers options. This feature is especially helpful if someone is doing research on a particular TF family. The see all search queries tab provides a list of the TF families with a description of their 3D structures and the protein sequences. Retana Ramirez and Basu The published genes tab gives a list of the TF family, Gen- Bank ID, name, and the PMID (PubMed citation ID) for all published genes. The GenBank ID takes the viewer directly to the NCBI webpage for the nucleotide sequence. The data- base also allows comparing TOBFAC sequences with Gen- Bank ID side by side by generating a spreadsheet. Some of the great features of this database are that sequences can be queried by BLAST searches, and also downloaded for fur- ther analysis. Similarly to other databases TOBFAC has tools to generate phylogenetic trees for TF families. The da- tabase is frequently updated and well maintained with it last update dated on January 2008. ATHAMAP (GERMANY) The AthaMap (http://www.athamap.de/) [14] is a data- base dedicated solely to Arabidopsis thaliana and contains a total of 109 TFs, potential TFs, and small RNA binding sites in Arabidopsis thaliana genome. A list of the 109 TFs can be located under the documentation tab. There are three main useful tools on the AthaMap website: search, colocalization, and gene analysis; all of these can be accessed by using the tool tab. The power of the search tool consists of being able to submit genomic position and get a TF binding site. This can be accomplished by entering genomic location or the Arabidopsis Genome Initiative (AGI) number. The colocali- zation tab provides the ability to identify colocalization of TF binding sites of pairs of TFs included in the AthaMap database. The gene analysis tool generates graphical repre- sentation of binding of many TF families with respect to any Arabidopsis gene. The overall setup of the website is very organized and helpful. Some of the weaknesses of the data- base are as follows. It is not possible to compare the database to other TF databases. Downloads are not possible which would have been very helpful. The TF coverage (109) is rather low compared to other databases. The strengths of the database are that it has the ability to provide information on potential TFs and small RNA binding sites, which are not common in other databases. It was last updated in June 2008, which is a great indication that it is a database that is often updated and well maintained. Overall this is a well put to- gether website but it is very specific as far as what it offers. DBD: TRANSCRIPTION FACTOR PREDICTION DA- TABASE (UK) The DBD: Transcription factor prediction database (http://www.transcriptionfactor.org) [15] contains the most extensive selection when it comes to the total number of ge- nomes (927) and the capacity to search for predicted TFs sites. The database has the capability to search by genomes list, or by TF families list. The Browse Genomes tab pro- vides names of the genomes, kingdoms, genomic sizes, number of available TFs etc. Selecting any given organism’s genome will redirect to a page with list of genes and their corresponding TF domains for the genes. The Browse Fam- ily tab includes a table with TF Family name, Family ID, HMM (Hidden Markov Model) ID [16], predicted TF do- main architecture, and taxonomic distribution. The taxo- nomic distribution link is an interesting and useful feature in this database. The taxonomic distribution link generates a graphical map of taxonomic distribution of a particular TF across the kingdom. This database is one of the most ambi-