iPE::State::AltSplice::MultiFivePrime(3)

NAME
iPE::State::AltSplice::MultiFivePrime - Multi 5' site state.

DESCRIPTION
This altsplice state looks for multiple 5' sites of any feature. If features overlap and contain multiple 5' sites, then a state is defined for both of these transcripts as being the MultiFivePrime state.

FUNCTIONS

detect (transcripts, seqLen)
    Detect the multi 5' sites in the passed array of annotations, and alter the annotation to contain these states.

    What we're looking for is this:

     =====|||||||||=====  1
     ====||||||||||=====  2
     ======||||||||=====  3

    Layer 1 and 2 can happen any number of times in the gene. We want to create two additional states, the first will be the space between 2's 5' end and 1's 5' end, and the second will be between 1's 5' end and 3's 5' end.

    All features which are on opposing strands will not be candidates for grouping into multi 5' sites.

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

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