iPE::State::AltSplice::OptExon(3)

NAME
iPE::State::AltSplice::OptExon - Optional exon altsplice state.

DESCRIPTION
This altsplice state is for optional exons, ones that exist in some isoforms but not in others. They have to be clearly

FUNCTIONS

detect (transcripts, seqLen)
    Detect optional exons in the passed array of transcripts annotating a sequence of underlying length seqLen.

     What we're looking for is this:

     ===|||||||||===||||||||======||||||||||====
     ==||||||||||=================||||||||||||==
                 <--------------->
                   supercassette

     Layer 1 and 2 can happen any number of times in the gene.  Fortunately for us, the annotation is divided up into same-annotated segments.

     Note that a longer intron is allowed in other isoforms.  That is, if another isoform skips this exon and other exons, we take the shortest version; the one with one segment per pre- and post- optional exon introns.

SEE ALSO
iPE::State::AltSplice iPE::State iPE::gHMM

AUTHOR
Bob Zimmermann (rpz@cse.wustl.edu)