Abstract: The surprisingly low number of about 25,000 genes in the human
genome  confirmed a fairly accurate estimate given by King and Jukes in
1969 based on population genetical arguments . On the other hand, the
number of different transcripts vastly exceeds gene number. This fact
intensified the search for alternatively spliced genes. Recent
results [1,3,4-7] suggest that more than 60% of the human genes are
alternatively spliced, some of them with a myriad of different splice forms.
Alternative splicing is found in all higher eukaryotic species in varying
frequency. In this paper we focus on a particular form of alternative splicing,
the so-called mutually exclusive exon usage (MEEU). In most known examples
mutually exclusive exons are arranged in cassettes of highly similar exons
suggesting that they have been derived by exon duplication [8-10]. Since
classical gene-finding programs may fail to correctly predict such
genes [11-16], we present a method, which is based on local
similarity of exons, to detect gene candidates with mutually exclusive exon
usage. We have screened the entire genome of D. melanogaster and found
five new genes with MEEU in addition to eight previously described cases.
Additional 1703 candidate regions of putative mutually exclusive exons were identified.