Table 1.
Information on Several Databases, Institutes, and Bioinformatics Tools
| Name of the Database, Bioinformatics Tool or Institute | Relevant Website Address | Comment and Relevant References |
|---|---|---|
| AGRIS (Arabidopsis Gene Regulatory Information Server) | http://arabidopsis.med.ohio-state.edu/ | Database for Arabidopsis promoter sequences and TFs and their target genes [18] |
| BLAST (Basic Local Alignment Search Tools) | http://blast.ncbi.nlm.nih.gov/Blast.cgi | Comparison of nucleotide or amino acid sequences from various organisms [19] |
| blastn | http://blast.ncbi.nlm.nih.gov/Blast.cgi | Comparison of nucleotide sequence against nucleotide sequence query |
| blastp | http://blast.ncbi.nlm.nih.gov/Blast.cgi | Comparison of a protein query against a protein database |
| blastx | http://blast.ncbi.nlm.nih.gov/Blast.cgi | Comparison of a protein database using a translated nucleotide query |
| CBI | http://www.cbi.pku.edu.cn/ | First bioinformatics center in China |
| EMBL (The European Molecular Biology Laboratory) | http://www.embl.de | EMBL is an international intergovernmental (Germany, UK, France, and Italy) research organization in Europe promoting molecular biology and genomics research [20] |
| EST (Expressed Sequence Tags) | www.ncbi.nlm.nih.gov/dbEST/ | A EST database is made from randomly sequenced cDNA clones [21, 22] |
| E-value | http://blast.ncbi.nlm.nih.gov/Blast.cgi | 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 |
| FASTA | http://www.ncbi.nlm.nih.gov/blast/fasta.shtml | It is a text format used to write protein or nucleotide sequences |
| GenBank | http://www.ncbi.nlm.nih.gov/Genbank/ | One of the largest genetic sequence databases containing records of 85,759,586,764 bases (as of September 4, 2008) [23] |
| IPGC (International Poplar Genome Consortium) |
http://www.ornl.gov/sci/ipgc/ | A consortium for post genomic sequence research on poplar [24] |
| JGI (Joint Genome Institute) | http://www.jgi.doe.gov/ | A US Dept. of Energy institute promoting research on genomics of various organisms |
| MIPS (Munich Information Center for Protein Sequences) |
http://mips.gsf.de | A database for nucleotide and protein sequences [25] |
| NCBI | http://www.ncbi.nlm.nih.gov/ | National Center for Biotechnology Information, Bethesda, Maryland, USA |
| Pfam | http://pfam.sanger.ac.uk/ | A database of proteins families represented by multiple sequence alignments and hidden Markov models [26] |
| Position-Specific Iterative BLAST (PSI-BLAST) | http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/psi1.html | Search for distantly related protein families |
| PubMed | http://www.ncbi.nlm.nih.gov/pubmed/ | A database of over 18 million citations |
| RAFL (RIKEN Arabidopsis full-length (RAFL) cDNA) | http://rarge.gsc.riken.jp/cdna/cdna.pl | A database to search for Arabidopsis full length cDNAs [27] |
| RARGE (RIKEN Arabidopsis Genome Encyclopedia) | http://rarge.gsc.riken.jp/ | A database for Arabidopsis genome [28] |
| RefSeq (The Reference Sequence collection) | 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] |
| RIKEN | http://rarge.gsc.riken.jp/index.html | A research foundation in Japan |
| SUPERFAMILY | http://supfam.org/SUPERFAMILY/ | A database containing structural and functional protein annotations from over 900 organisms [30] |
| TAIR (The Arabidopsis Information Resource) | http://www.arabidopsis.org | A comprehensive resource for Arabidopsis genome [31] |
| tblastn | http://blast.ncbi.nlm.nih.gov/Blast.cgi | Comparison of a protein query sequence against a nucleotide sequence database |
| tblastx | http://blast.ncbi.nlm.nih.gov/Blast.cgi | tblastx converts a nucleotide query sequence into protein sequences and the resulting sequences are compared to search for homologous regions |
| TIGR (The Institute for Genomic Research) | http://www.tigr.org/ | Previously known as The Institute for Genomic Research, currently known as the J. Craig Venter Institute located in Rockville, Maryland, USA |
| TRANSFAC | http://www.gene-regulation.com/pub/databases.html | TF database [32] |
| UniGene | http://www.ncbi.nlm.nih.gov/UniGene/ | A database of transcriptome of many organisms, maintained by NCBI [33] |
| UniProt (The Universal Protein Resource) | http://www.uniprot.org/ | Protein sequence database [34] |