MOTIVATION: Prediction of gene structure in newly sequenced DNA becomes very 
important in large genome sequencing projects. This problem is complicated due 
to the exon-intron structure of eukaryotic genes and because gene expression is 
regulated by many different short nucleotide domains. In order to be able to 
analyse the full gene structure in different organisms, it is necessary to 
combine information about potential functional signals (promoter region, splice 
sites, start and stop codons, 3' untranslated region) together with the 
statistical properties of coding sequences (coding potential), information about 
homologous proteins, ESTs and repeated elements.
RESULTS: We have developed the GeneBuilder system which is based on prediction 
of functional signals and coding regions by different approaches in combination 
with similarity searches in proteins and EST databases. The potential gene 
structure models are obtained by using a dynamic programming method. The program 
permits the use of several parameters for gene structure prediction and 
refinement. During gene model construction, selecting different exon homology 
levels with a protein sequence selected from a list of homologous proteins can 
improve the accuracy of the gene structure prediction. In the case of low 
homology, GeneBuilder is still able to predict the gene structure. The 
GeneBuilder system has been tested by using the standard set (Burset and Guigo, 
Genomics, 34, 353-367, 1996) and the performances are: 0.89 sensitivity and 0.91 
specificity at the nucleotide level. The total correlation coefficient is 0.88.
AVAILABILITY: The GeneBuilder system is implemented as a part of the WebGene a 
the URL: http://www.itba.mi. cnr.it/webgene and TRADAT (TRAncription Database 
and Analysis Tools) launcher URL: http://www.itba.mi.cnr.it/tradat.