MOTIVATION: A number of programs have been developed to predict the eukaryotic 
gene structures in DNA sequences. However, gene finding is still a challenging 
problem.
RESULTS: We have explored the effectiveness when the results of several 
gene-finding programs were re-analyzed and combined. We studied several methods 
with four programs (FEXH, GeneParser3, GEN-SCAN and GRAIL2). By HIGHEST-policy 
combination method or BOUNDARY method, approximate correlation (AC) improved by 
3-5% in comparison with the best single gene-finding program. From another 
viewpoint, OR-based combination of the four programs is the most reliable to 
know whether a candidate exon overlaps with the real exon or not, although it is 
less sensitive than GENSCAN for exon-intron boundaries. Our methods can easily 
be extended to combine other programs.
AVAILABILITY: We have developed a server program (Shirokane System) and a client 
program (GeneScope) to use the methods. GeneScope is available through a WWW 
site (http://gf.genome.ad.jp/).
CONTACT: (katsu,takagi)@ims.u-tokyo.ac.jp