Comparative Analyses of Plant Transcription Factor Databases tion such as gene model, TF description and domain. Addi- tionally the database also provides information about ge- nome databases, orthologs and co-orthologs, domain archi- tecture (start codon, stop codon, and e-value), protein, and transcription sequences associated with each TF family. An- other way the database can be used is through the table of TFs family that lead to a description of the family character- istics and a list of all the species that contain this TF family. The website allows for BLAST search through the PubMed engine. The download link could be used to search for pro- tein sequence, TF domain architecture, transcription se- quence, and a list of TFs. The most convenient use of this database is being able to select a specific TF family and find which plant species is included in that TF family. It has a great verity of plant species that include rhodophyte, prasi- nophyte, chlorophyte, bryophyte, monocot, and eudicot. A minor pitfall in the database is the website has no indication of when it was last updated which tend to be a useful fact to know in plant genomics field which is moving at accelerated speed when it comes to new data publications. Overall this site is very effective in providing a good sample of plant TFs from several plant species that are not common amongst other databases. PLANT CARE (BELGIUM) The Plant Cis-Acting Regulatory Element (CARE) or Plant CARE (http://bioinformatics.psb.ugent.be/webtools/ plantcare/html/) [8] is a database that contains data accessi- ble freely for academia users. The site contains 435 plant transcription sites from monocots, dicots and other plants. Additionally more than 159 plant promoters are described. The main homepage include a ‘Query Care search’ for in- formation on a cis-acting regulatory site. The user can search broadly or narrowly for information by changing search pa- rameters when performing the search. Another option is searching for cis-acting regulatory sites present in promoter sequences. Other query options include searching for TFs from supergroups (e.g. eukaryotes) to all the way down to a species (e.g. Arabidopsis). One can search by gene name or by name of a TF. A search can be done under ‘Referencia’ for TF related papers relevant to Plant CARE. Some of the strengths of this database are the new features it offers, a ‘Motif sampler’, which consists of searching for regulatory element in a dataset of co-regulated promoter sequences, and also includes clustering of microarray [9] data. When com- paring this database with others, it can be rated as a useful one if looking for information for monocot, dicot, and more specifically cis-acting regulators. The database however does not list names of all the TFs like other databases. One of the weaknesses of this database is it does not list specifically what gene families or plant species form part of the TF data- base; first the user needs to search for a TF and then only the user knows what plant species is included in that particular TF family. The website does not have a feature to download or provide links to other databases. The link ‘Enter new data’ is also a non-functional link. PLACE (JAPAN) The PLACE or Plant cis-acting Regulatory DNA Ele- ments database (http://www.dna.affrc.go.jp/PLACE/index. Current Genomics, 2009, Vol. 10, No. 1 13 html) [10] consists of plant cis-acting regulatory DNA ele- ments mainly for vascular plant only, but the database has recently started to include cis elements information from Chlamydomonas reinhardtii too. Overall the website is very clearly put together which ensures quick navigation. The following searches are possible: by keyword, homology search by FASTA formats etc. The signal scan search and homology search can be used to find motifs identical or simi- lar to previously reported cis element motifs. Nucleotide sequences can be entered (or copied and pasted) in this data- base by selecting the signal scan search file upload tab and the resulting page will predict and show all putative TFs for that sequence. The database is a good resource to find cis elements. One of the most attractive features is the way the database is maintained up to date by inclusion of relevant research papers and adding them to the database. The data- base does not have download features but gives information on where they can be obtained. A big disadvantage of this database is the database maintenance was permanently ceased on February 2007. This database would be helpful if the researcher is looking for plant cis acting elements and already have a gene ID, PubMed ID numbers, or GenBank nucleotide sequence ID numbers. As time progresses the database will become eventually outdated, but at this mo- ment it still contains very relevant and useful information. DATABASE OF ARABIDOPSIS FACTORS (DATF) (CHINA) TRANSCRIPTION The Database of Arabidopsis Transcription Factors (DATF) (http://datf.cbi.pku.edu.cn/) [11] is entirely dedi- cated to Arabidopsis thaliana TFs. Some of the best features of the database include the classification of all TFs into 64 families which are accessible from the homepage of the website. The family organization of all the TFs has multiple elements of the DNA-binding domain and neighbor-joining phylogenetic trees of each family. Similarly to other data- bases this one contains a homolog tab with the rice TF data- base DRTF (discussed later). Additionally it contains infor- mation of about 1200 TFs, protein domains, and 3D structure information. One can search by either TF family or by chro- mosome. There is a link from the homepage on how to ac- cess other databases such as rice (DRTF), poplar (DPTF), and Plant Transcription Factor Databases, China (http:// planttfdb.cbi.pku.edu.cn/). Information provided for a given TF family consists of family introduction, family structure, and family binding sites. The following information can be downloaded: sequences of the family genomic sequence, CDS sequence, and protein sequence. Under the specific TF family, it is also possible to generate phylogenetic trees with genes in each TF family using the ‘Phylogenetic Tree JPG Image’ tool. One can also align the amino acid sequences encoded by genes of a TF family by choosing the ‘Multi- alignment’ option. A list of the total family ‘loci’ and ‘gene model’ are listed under each family. The gene models are organized in a table setup similar to the family class, making it an easy way to look through the information. This is a great database but its weaknesses are that it is only for one plant species and the last update for the database was in July 2006. Overall it would be considered an effective database used for Arabidopsis thaliana.