cDNA2Genome: A TOOL FOR MAPPING AND ANNOTATING cDNAS

The aim of a high-quality annotation is to identify the key genome features - in particular, the genes and their products in order to bridge the considerable gap between large-scale data-collection and its interpretation. The tools and resources for annotation are developing rapidly, however, high throughput data analysis requires the correct combination of these applications and databases.

In this context we have developed different analysis tools for semi-automatical annotation of sequences. In collaboration with other NGFN/DHGP research groups we have designed tools supporting cDNA mapping and characterization of full length cDNAs (cDNA2Genome). cDNA2Genome is a web tool for automatic high-throughput mapping and characterization of cDNAs. It uses already existing annotation data and improves them when possible with the most up-to-date databases, especially in the case of ESTs, proteins and mRNAs. cDNA2Genome is focussed on the determination of the cDNA exon-intron structure which is exhaustively assessed with a vast number of approaches to gene prediction. The final result of cDNA2Genome is an XML file which contains all relevant information obtained by the task. This XML output can be easily used in successive analysis (i.e. in pipelines or for integrating the data into databases). At the same time, the web user can easily inspect the xml output through the graphical display using standard web browsers. The graphical representation provides an interactive view of the annotations. The complete application outputs are immediatly accessible via hyperlinks.