DBD: Transcription factor prediction database

Release 2.0
www.transcriptionfactor.org
Sequence ID search:
News
Updates to DBD
9th Nov 2011 A new bacterial genome is added:
Pedobacter Heparinus.
30th Aug 2008 New fungal genomes: added TF predictions for 5 new fungal genomes:
Schizosaccharomyces octosporus yFS286, Verticillium dahliae VdLs.17, Verticillium albo-atrum VaMs.102, Schizosaccharomyces pombe 972h- and Aspergillus fumigatus A1163.
20th Aug 2008 Integrated transcription factor predictions for the Dictyostelium purpureum genome from the JGI.
The dictyostelids are a group of cellular slime molds, or social amoebae, which belong to the amoebozoa supergroup of eukaryotes that form a sister clade to the fungi and animals. Under normal growth conditions the dictyostelids take the individual amoeba form, but under starvation they from multicellular organisms. Further details.
18th Aug 2008 Added TF predictions for over 50 bacterial genomes from the NCBI.
Highlights include, the first genome to be sequenced from a novel bacterial phylum, comprising endosymbionts of cellulose-degrading termite gut protozoa (Endomicrobia) Elusimicrobium minutum Pei191, new genomes from the Verrucomicrobia phyla Akkermansia muciniphila ATCC BAA-835, Methylacidiphilum infernorum V4 and the Aquificae phyla Sulfurihydrogenibium sp. YO3AOP1, Hydrogenobaculum sp. Y04AAS1.
11th Aug 2008 Reclassified 8 domains.
Added 3 families to list of DBDs. From Pfam: added SpoVT_AbrB (PF04014), NAM (PF02365), Pencillinase (PF03965).
Removed 6 familes from list of DBDs. From Pfam: removed Bac_DnaA_C (PF08299), C1_4 (PF07975), and from SUPERFAMILY: Hemolysin expression modulating protein HHA superfamily (68990), Hypothetical protein F93 family (109674), Transcriptional regulator Rrf2 family (109699).
8th Aug 2008 Transcription factor predictions for new green algae Ostreococcus RCC809.
3rd July 2008 Transcription factor predictions for 2 new fungal genomes: Trichoderma atroviride and Cochliobolus heterostrophus.
20th June 2008 Loaded transcription factor predictions for microalgae Chlorella sp. NC64A.
3rd June 2008 Added 8 Eukaryotic genomes, and updated 12 drosophilid genomes.
Including several newly sequenced fungal strains such as the Chytridiomycota Batrachochytrium dendrobatidis JAM81.
12th May 2008 Added the transgenic papaya (Carica papaya) genome, and over 50 prokaryote genomes.
Highlights among the prokaryote genomes include the first genome from the Verrucomicrobia phyla (Opitutus terrae) of bacteria, and the first genome from the Korarchaeota phyla (Candidatus Korarchaeum cryptofilum) of archaea.
30th Apr 2008 Added the phytoplankton Emiliania huxleyi, which is of interest because of it's production of polyketides with antimicrobial, antifungal, antiparasitic, antitumor and agrochemical properties. Updated the beetle Tribolium castaneum assignments as analysis of the genome sequence recently became available [PubMed]. Updated the Schizosaccharomyces pombe genome.
28th Apr 2008 Major update of all Ensembl genomes, including new genomes: Horse and Orangutan.
11th Apr 2008 Loaded 2 new early assembly plant genomes: Glycine max (Soybean) and Zea mays (Maize).
31st Mar 2008 Added new plant genome from the JGI: Sorghum bicolor.
21st Feb 2008 Reclassified 1 domain: Added Copper-fist to list of DBDs.
18th Feb 2008 Added 2 new algae genomes from the JGI:
Micromonas sp. RCC299, Micromonas sp. CCMP490.
23rd Jan 2008 Added 3 fungal and 59 prokaryotic genomes.
10th Jan 2008 Added 1 plant and 7 fungal genomes:
Selaginella moellendorffii (Spikemoss), Vanderwaltozyma polyspora, Podospora anserina, Trichoderma virens, Saccharomyces cerevisiae YJM789, Saccharomyces cerevisiae RM11-1a, Cryptococcus neoformans var. grubii H99, Cryptococcus neoformans B-3501A.
18th Dec 2007 Updated the mouse genome and added 2 new animal genomes:
Microcebus murinus (mouse lemur), Ochotona princeps (American pika)
11th Dec 2007 DBD database update article now online. Please cite:

DBD - taxonomically broad transcription factor predictions: new content and functionality

Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, Sarah A. Teichmann
Nucleic Acids Research 2008 36(Database issue):D88-D92; doi:10.1093/nar/gkm964
Abstract [ PubMed ]   Full text [ HTML · PDF ]  
Download citation [ RIS (for EndNote, Reference Manager, ProCite) · BibTeX ]

1st Nov 2007 Added 10 new Eukaryotic genomes:
Aureococcus anophagefferens, Trichoplax adhaerens, Xenopus laevis, Helobdella robusta, Nasonia vitripennis, Mycosphaerella fijiensis, Vitis vinifera, Giardia lamblia, Toxoplasma gondii, Capitella sp. I.
17th Oct 2007 DBD database update article accepted by Nucleic Acids Research editor.
3rd Oct 2007 Completed inclusion of 200 new, and 100 updated, prokaryotic genomes.
3rd Aug 2007 Reclassified 4 domains: Added CG-1 and Churchill domains to list of DBDs, and removed ARID (Pfam, SUPERFAMILY) and SOH1 domains from list of DBDs.
9th July 2007 DBD database update article proposal accepted by Nucleic Acids Research database issue editor.
9th July 2007 Added new low coverage Eukaryotic genomes from Ensembl, fungal genomes from FGI and basal metazoa from JGI.
Highlights include the sea anemone Nematostella vectensis, crustacean Daphnia pulex , moss Physcomitrella patens subsp. patens and the colony forming algal species Volvox carteri f. nagariensis.
22nd June 2007 Added ability to browse predicted transcription factors with similar domain combinations to the detailed transcription factor pages.
12th Mar 2007 Updated to current (43.36e) Ensembl homo sapiens genome.
7th Feb 2007 Installed new disk drive in DBD server.
19th Jan 2007 Added search for DBDs in organsims.
4th Jan 2007 Added 11 AAA drosophilid genomes to DBD database and web site:
Drosophila erecta, Drosophila grimshawi, Drosophila virilis, Drosophila yakuba, Drosophila sechellia, Drosophila pseudoobscura, Drosophila ananassae, Drosophila mojavensis, Drosophila willistoni, Drosophila persimilis, Drosophila simulans.