Bioinformatics, Vol 15, 612-621, Copyright © 1999 by Oxford University Press
L Milanesi, D D'Angelo and IB Rogozin
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.
ARTICLES
GeneBuilder: interactive in silico prediction of gene structure
Istituto di Tecnologie Biomediche Avanzate CNR, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy. milanesi@itba.mi.cnr.it
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