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

[Sitaram Rajaraman]

Thank you ! I will proceed with this information !

- Sitaram.

On 03/11/2013 04:51 PM, Carson Holt wrote:
> 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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>


-- 
Sitaram Rajaraman,
Plant Stress Research Group,
Dept of Biosciences,
University of Helsinki.