Retana Ramirez and Basu (Table 1) contd…. Relevant Website Address Comment and Relevant References http://rarge.gsc.riken.jp/index.html http://supfam.org/SUPERFAMILY/ A research foundation in Japan A database containing structural and functional protein annotations from over 900 organisms [30] http://www.arabidopsis.org A comprehensive resource for Arabidopsis genome [31] http://blast.ncbi.nlm.nih.gov/Blast.cgi http://blast.ncbi.nlm.nih.gov/Blast.cgi http://www.tigr.org/ http://www.gene- regulation.com/pub/databases.html http://www.ncbi.nlm.nih.gov/UniGene/ Comparison of a protein query sequence against a nucleotide sequence database tblastx converts a nucleotide query sequence into protein sequences and the resulting sequences are compared to search for homologous regions Previously known as The Institute for Genomic Research, currently known as the J. Craig Venter Institute located in Rockville, Maryland, USA TF database [32] A database of transcriptome of many organisms, maintained by NCBI [33] http://www.uniprot.org/ Protein sequence database [34] 12 Current Genomics, 2009, Vol. 10, No. 1 Name of the Database, Bioinformatics Tool or Institute RIKEN SUPERFAMILY TAIR (The Arabidopsis Information Resource) tblastn tblastx TRANSFAC UniGene TIGR (The Institute for Genomic Research) UniProt (The Universal Protein Resource) PLANT (CHINA) TRANSCRIPTION FACTOR DATABASES The Plant Transcription Factor Databases (http://planttfdb. cbi.pku.edu.cn/) [6] provide information for putative TFs of the following plant species, namely, Arabidopsis thaliana, Populus trichocarpa, and Oryza sativa. It also contains TF sequence information of Chlamydomonas reinhardtii, and Physcomitrella patens. Additionally it contains databases based on the available EST sequences from 17 other plant species: (maize, barley, wheat, sorghum, sugarcane, upland cotton, soybean, potato, apple, sweet orange, grape, sun- flower, barrel medicago, lotus, loblolly pine, and white spruce). In the main homepage there is introductory informa- tion that familiarizes the viewer with what is offered by the database. Strengths of this database are it includes important information about each TF family and goes well in depth as far as giving the functional domains for each TF. Another positive aspect of this database is it includes citations associ- ated with each individual TF family. This database takes it a step further by displaying TF entries of what other databases like UniProt, RefSeq, and TransFac have. Information such as TF family and associated genes can be accessed by select- ing a plant species and then can be browsed by family or by chromosome. Once the TF family is selected the next choice is by gene. The gene information consists of some basic in- formation, gene structure, annotation, protein sequence fea- tures, 3D structure, ontology, expression, sequence, and ref- erences on other databases. All the information given by selecting each gene is very well organized and visually ap- pealing to the viewer. In the main homepage, it is important to note that each plant species has a database and a page of its own that opens when selected. The BLAST option will provide different types of blast searches like blastp, blastn, blastx, and tblastn. For each BLAST option, it is possible to choose one of the 22 plant species. The search option takes to sub-databases by selecting specific species. A great asset of this website is the fact that it has a large number of differ- ent species that can be viewed and selected even if 17 of them do not have a complete genome sequenced. Available downloads include protein sequences files, CDS (coding sequence) sequences files, and ortholog prediction files. The overall website is well organized, and maintained; last re- vised in May 14, 2008. PLANT TRANSCRIPTION (GERMANY) FACTOR DATABASE The Plant Transcription Factor Database (http://plntfdb. bio.uni-potsdam.de/v2.0/) [7] provides TF data for three plant species (Oryza sativa subsp. japonica, Arabidopsis thaliana, and Populus trichocarpa) and for Chlamydomonas reinhardtii, Cyanidioschyzon merolae, Ostreococcus tauri, and Physcomitrella patens also. The database compiles a total of 68 TF families. The outline of the homepage is a table of all the TF families followed by a table of other tran- scriptional regulators. It is also possible to search the data- base by sequence identifier or by gene ID. When selecting one of the seven plant species link, it will go directly to a page in which it contains information on TF families associ- ated with that particular plant species. For that given family of TFs there are series of links that reveal important informa-