The goal of the TRADAT project was to develop an integrated platform of databases and software tools for the analysis of regulatory genomic DNA. The proposed contribution of our group was to maintain and expand the Eukaryotic Promoter Database EPD and to develop novel computer methods to design informative experiments to characterise transcription factor binding sites.
Overall, the TRADAT project has reached its objectives, as documented by its website (http://web.archive.org/web/20050204102902/http://www.itba.mi.cnr.it/tradat/). The main achievements of our groups were the following: (i) the introduction of a new format of EPD allowing for the representation of many new types of information, including links to other databases; (ii) the development of novel, user-friendly, web-based interfaces for accessing EPD, including the SEView applet viewer which enables the user to navigate from EPD to EMBL to SWISS-PROT within the same graphic environment; (iii) the development of two new computer programs to design training and test oligonucleotide sequence sets for the refinement and experimental validation of generalised profile-based algorithms to predict the affinity of transcription factor binding sites. These tools had an impact on biological research beyond the scope of the TRADAT project. EPD has played an instrumental role in the development of promoter prediction algorithms by research teams all over the world. The SEView applet developed for TRADAT has found applications in other fields, for instance as a viewer of protein domain structures. The programs developed for designing the oligonucleotide sequences for the CTF/NF-1 binding experiments have been used for another project aimed at characterizing STAT protein binding sites. The experience gained in maintaining compatibility between asynchronously updated federated databases and the research conducted on this topic turned out to be very helpful in developing two new databases of predicted protein sequences, TREST and TRGEN (available from
ftp://ftp.ch.embnet.org). Public tools developed by our group under this project are available from the EPD website (http://www.epd.isb-sib.ch).
