DATFAP: A Database of Primers and Homology Alignments for Transcription Factors from 13 Plant Species

BackgroundMany well-known transcription factor databases do not provide PCR primers for the sequences. Often, transcription factors from the same family have a very high sequence similarity, and so specific primer sets that only amplify their targets and none of the other family members may be hard to design manually. Also, it may often be useful to have one general primer set targeting the slightly different homologs of some transcription factor from several species.ResultsDATFAP is a free, web-based, very user-friendly browsing tool based on a new database of more than 55,000 EST sequences from 13 plant species, classified as transcription factors. Further, the database offers primers designed for RealTime-PCR as well as homology alignments and phylogenies for the sequences. The provided PCR primers are designed so that they have a perfect sequence alignment to their target only and not to any other sequences in the database from the same species. Via a direct link to a helper tool, the user may also design a general primer set targeting all sequences in any hand-picked group of homologs. A sophisticated search facility enables the user to find exactly the relevant sequences which subsequently may be easily downloaded. All homologies among the more than one billion possible pairwise sequence comparisons of DATFAP have been charted in advance. Thus, the user may quickly display the alignment of any sequence and all its database homologs.ConclusionBecause of the comprehensive homology analysis, it is very easy to find related transcription factors from different species, i.e. to navigate the network of inter-related transcription factors from the different species, and to find specific or general primers for them. DATFAP is found at the project homepage.

[1]  J. Memelink,et al.  Genetic modification of plant secondary metabolite pathways using transcriptional regulators. , 2001, Advances in biochemical engineering/biotechnology.

[2]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[3]  John Quackenbush,et al.  The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes , 2004, Nucleic Acids Res..

[4]  Jakob Fredslund,et al.  Primique: automatic design of specific PCR primers for each sequence in a family , 2007, BMC Bioinformatics.

[5]  Jakob Fredslund,et al.  PHY·FI: fast and easy online creation and manipulation of phylogeny color figures , 2006, BMC Bioinformatics.

[6]  Mark Stitt,et al.  Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes. , 2004, The Plant journal : for cell and molecular biology.

[7]  F. Corpet.  Multiple sequence alignment with hierarchical clustering. , 1988, Nucleic acids research.

[8]  Masakazu Satou,et al.  RARTF: database and tools for complete sets of Arabidopsis transcription factors. , 2005, DNA research : an international journal for rapid publication of reports on genes and genomes.

[9]  Ingo Dreyer,et al.  PlnTFDB: an integrative plant transcription factor database , 2007, BMC Bioinformatics.

[10]  B. Mueller‐Roeber,et al.  A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors , 2007, Plant Methods.

[11]  Ncbi.  National Center for Biotechnology Information , 2008 .

[12]  R. Mittler,et al.  Could heat shock transcription factors function as hydrogen peroxide sensors in plants? , 2006, Annals of botany.

[13]  Di Liu,et al.  DATF: a database of Arabidopsis transcription factors , 2005, Bioinform..

[14]  Xin Chen,et al.  PlantTFDB: a comprehensive plant transcription factor database , 2007, Nucleic Acids Res..

[15]  Jakob Fredslund,et al.  PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs , 2005, Nucleic Acids Res..

[16]  E. Huq,et al.  The Arabidopsis Basic/Helix-Loop-Helix Transcription Factor Family Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.013839. , 2003, The Plant Cell Online.

[17]  R. R. Samaha,et al.  Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes. , 2000, Science.