Comparative Analyses of Plant Transcription Factor Databases Current Genomics, 2009, Vol. 10, No. 1 11 Table 1. Information on Several Databases, Institutes, and Bioinformatics Tools Relevant Website Address Comment and Relevant References Name of the Database, Bioinformatics Tool or Institute AGRIS (Arabidopsis Gene Regulatory Informa- tion Server) BLAST (Basic Local Alignment Search Tools) EMBL (The European Molecular Biology Laboratory) EST (Expressed Sequence Tags) IPGC (International Poplar Genome Consortium) JGI (Joint Genome Institute) MIPS (Munich Information Center for Protein Sequences) http://blast.ncbi.nlm.nih.gov/Blast.cgi Comparison of nucleotide sequence against nucleotide sequence query http://blast.ncbi.nlm.nih.gov/Blast.cgi Comparison of a protein query against a protein database http://blast.ncbi.nlm.nih.gov/Blast.cgi Comparison of a protein database using a translated nucleotide query Database for Arabidopsis promoter sequences and TFs and their target genes [18] Comparison of nucleotide or amino acid sequences from various organisms [19] First bioinformatics center in China EMBL is an international intergovernmental (Germany, UK, France, and Italy) research organization in Europe promoting molecular biology and genomics research [20] A EST database is made from randomly sequenced cDNA clones [21, 22] E-value determines the stringency of a blast search, lower e-value means good match with the query sequence and an e-value of 0 (zero) means 100% match with the query sequence It is a text format used to write protein or nucleotide sequences One of the largest genetic sequence databases containing records of 85,759,586,764 bases (as of September 4, 2008) [23] blastn blastp blastx CBI E-value FASTA GenBank NCBI Pfam PubMed Position-Specific Iterative BLAST (PSI-BLAST) http://www.ncbi.nlm.nih.gov/Education/B LASTinfo/psi1.html http://arabidopsis.med.ohio-state.edu/ http://blast.ncbi.nlm.nih.gov/Blast.cgi http://www.cbi.pku.edu.cn/ http://www.embl.de www.ncbi.nlm.nih.gov/dbEST/ http://blast.ncbi.nlm.nih.gov/Blast.cgi http://www.ncbi.nlm.nih.gov/blast/fasta.s html http://www.ncbi.nlm.nih.gov/Genbank/ http://www.ncbi.nlm.nih.gov/ http://pfam.sanger.ac.uk/ http://www.ornl.gov/sci/ipgc/ A consortium for post genomic sequence research on poplar [24] http://www.jgi.doe.gov/ A US Dept. of Energy institute promoting research on genomics of various organisms http://mips.gsf.de A database for nucleotide and protein sequences [25] National Center for Biotechnology Information, Bethesda, Maryland, USA A database of proteins families represented by multiple sequence alignments and hidden Markov models [26] Search for distantly related protein families RAFL (RIKEN Arabidopsis full-length (RAFL) cDNA) RARGE (RIKEN Arabidopsis Genome Encyclopedia) RefSeq (The Reference Sequence collection) http://www.ncbi.nlm.nih.gov/pubmed/ A database of over 18 million citations http://rarge.gsc.riken.jp/cdna/cdna.pl A database to search for Arabidopsis full length cDNAs [27] http://rarge.gsc.riken.jp/ A database for Arabidopsis genome [28] http://www.ncbi.nlm.nih.gov/RefSeq/ A database of well annotated DNA, protein and transcript sequences developed from genomic information from diverse organisms [29]