GeneFinder does not directly take into account splice branch sites when
predicting genes. However it is possible to give GeneFinder branch
site information by supplying splice acceptor sites which are a
combination of splice branch and acceptor. The combined
branch/acceptor motifs are located in the sequence by a program called
Sp3splice which is external to ACEDB, and the results are written to a
file with the ".useg" extension. Note that "useg" is a contraction of User
Segments. The following example is a demonstration of the value of
including splice branch information for predicting genes in S.
pombe
Bring up the fmap for Test_Sequence EM:X56564 and choose [GeneFinder
features] followed by [AutoFind gene] from the GeneFind.. menu. The
predicted gene is not the same as the gene from the EMBL record (see
below).
Select [GeneFinder parameters] from the GeneFind.. menu and change
3-splice cutoff to 2.00 (see below). Splice acceptors calculated by
GeneFinder do not attain scores over 2.00, so this ensures that they
are not used. Now select [GeneFinder features] from the GeneFind..
menu and notice that all the acceptors have disappeared from the fmap.