DATFAP: A Database of Primers and Homology Alignments for Transcription Factors from 13 Plant Species
BiRC – Bioinformatics Research Center, University of Aarhus, Høegh-Guldbergs Gade 10, Building 1090, DK-8000 Århus C, Denmark
BMC Genomics 2008, 9:140 doi:10.1186/1471-2164-9-140Published: 25 March 2008
Many 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.
DATFAP 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.
Because 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.