[maker-devel] Doubts in the synthesis part of MAKER

[Carson Holt]

Hints are basically CDS location, exon location, and intron location.  The
CDS hints are based on protein alignment.  Intron and exon hints are based
on the EST alignments, which when polished should give exact intron
coordinates.  Ironically the most useless part of the gene model is
actually the most informative feature for gene prediction (the intron
coordinates).

lib/Process/MPIchunk.pm will have the steps in the _go method.  It is a
little hard to follow as MAKER is designed for distributed parallelization
(i.e. parallelization without shared memory with steps potentially divided
on different machines on the other end of the network).

It is divided into MPItier and MPIchunk objects.  The MPItier object
encapsulate a series of linear steps or 'levels' while the MPIchunk
objects encapsulate a single step sent to a machine across the network and
it exists within a single 'level' of the MPITier object.  Note there can
be multiple chunks assigned to a 'level'.  MPItiers can also have MPITiers
as children at a given level instead of MPIchunks, so the process
structure then branches like a tree and can then merges back somewhere in
the middle of the algorithm.

The 'maker' script is really just the communication script for the
objects.  In MPI one maker thread is launched to handle communication and
another to run the MPItiers and MPIchunks.  They communication threads
then pass MPIchunks and MPITiers back and forth across the network by
either requesting things to do from other nodes or by asking for help if
they have a large number of MPIChunks or MPItiers to process.

Thanks,
Carson





On 13-03-11 10:33 AM, "Sitaram Rajaraman" <sitaram.rajaraman at helsinki.fi>
wrote:

>Hello MAKER developers,
>			I'm Sitaram, working as a Bioinformatician at the University of
>Helsinki. We are trying out MAKER as part of a gene prediction/annotation
>pipeline and have some doubts regarding this. In the synthesis step in
>the paper, I find it a bit hard to visualise how the hints are generated
>from the various sources and the scores are calculated. It would be nice
>if you could throw some light on this. Also if you could point to the
>particular .Pm file which contains the actual source code, it would be
>convenient as there quite a lot of source code and debugging the whole
>set is bit cumbersome.
>
>Regards,
>
>-- 
>Sitaram Rajaraman,
>Plant Stress Research Group,
>Dept of Biosciences,
>University of Helsinki.
>
>
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