IDENTIFICATION OF TRANSCRIBED SEQUENCES: MORE CHALLENGES?

Stefan Wiemann
Dept. Molecular Genome Analysis
Genomics&Proteomics
German Cancer Research Center
Im Neuenheimer Feld 506
69120 Heidelberg
Germany
telephone: +49 6221 42 4702
fax: +49 6221 4252 4702
email: s.wiemann@dkfz.de
prestype: Platform
presenter: Stefan Wiemann

Stefan Wiemann, Ruth Wellenreuther, Petra Heidrich, Regina Albert, Ingo Schupp, Vladimir Kuryshev, Jiancong Xu, Jeremy Simpson², Rainer Pepperkok², Annemarie Poustka and the German cDNA Consortium
¹Molecular Genome Analysis, German Cancer Research Center, Im Neuenheimer Feld 506, D-69120 Heidelberg, Germany
²Cell Biology Program, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany

We have formed a network in the frame of the German Genome Project aiming at the generation and sequencing of novel full-length cDNAs, and the comprehensive functional analysis the deduced proteins. The project started in September 1997. Over 4,500 cDNAs (> 11.6 Mb) have been sequenced since. The set of fully sequenced clones in combination with EST-sequenced clones is used to generate a minimal set of full-length clones for employment in subsequent functional analysis. A progress report of the network activities and achievements will be presented.

Using the full-length cDNAs in a systematic analysis of gene predictions, which are based on genomic sequence, we observe that most (>90%) gene predictions do not correctly annotate the true 5'-end of coding regions. As a consequence the amplification of ORFs that are based on gene predictions is not reliable enough to obtain the majority of protein coding regions. The analysis of full-length cDNAs, therefore, still remains the method of choice for correctly identifying complete protein coding sequences.