Read Segments

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.

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