Affiliations: Göttingen Genomics Laboratory, Institut für
Mikrobiologie und Genetik, Grisebachstrasse 8, D-37077 Göttingen, Germany.
Tel.: +49 551 39 3823; Fax: +49 551 39 3805. Abteilung Allgemeine
Mikrobiologie, Institut für Mikrobiologie und Genetik | Abteilung Molekulare Genetik und Präparative
Molekularbiologie, Institut für Mikrobiologie und Genetik E-mail:
Note:  Corresponding author
Abstract: The performance of gene-predicting tools varies considerably if
evaluated with respect to the parameters sensitivity and specificity or their
capability to identify the correct start codon. We were interested to validate
tools for gene prediction and to implement a metatool named YACOP, which
combines existing tools and has a higher performance. YACOP parses and combines
the output of the three gene-predicting systems Criticia, Glimmer and ZCURVE.
It outperforms each of the programs tested with its high sensitivity and
specificity values combined with a larger number of correctly predicted gene
starts. Performance of YACOP and the gene-finding programs was tested by
comparing their output with a carefully selected set of annotated genomes. We
found that the problem of identifying genes in prokaryotic genomes by means of
computational analysis was solved satisfactorily. In contrast, the correct
localization of the start codon still appeared to be a problem, as in all cases
under test at least 7.5% and up to 32.3% of the positions given in the
annotations differed from the locus predicted by any of the programs tested.
YACOP can be downloaded from http://www.g2l.bio.uni-goettingen.de.