[Gmod-help] Re: [Gmod-gbrowse] Best practices for generating alignments for GBrowse...

[Josh Goodman]

Hi Bob and Dave,

I'm not directly involved in the assembly migration tasks.  Thus, your best bet is to contact the
FlyBase Harvard group who is responsible for these tasks and can explain exactly what is done and
what if anything they can provide.  I'll send you their contact info off list.

Sorry I can't be more helpful than that.

Cheers,
Josh

Dave Clements, GMOD Help Desk wrote:
> Hi Bob, Josh, and all MAKER folk,
> 
> One of the sessions at the Americas summer school was on MAKER, an
> annotation pipeline for eukaryotes.  I believe that MAKER can do most,
> possibly all, of what you need, and it produces GFF3 to boot.  I've
> CC'd the MAKER list for confirmation (or denial :-).
> 
> Your second question was: how do people deal with incremental updates
> of assemblies?  This came up at the just finished August 2009 GMOD
> Meeting.  Josh Goodman of FlyBase indicated that they had a set of
> programs that compared the two assemblies and programmatically moved
> annotations from the old to the new for almost all annotations.  For
> each migration there are also a small number of annotations that are
> flagged for manual curation and these are looked at by FlyBase
> curators.
> 
> Josh, do you know if the FlyBase process might be made available
> outside of FlyBase?  Would it be useful outside of FlyBase?
> 
> Do other communities have scripts for doing this type of migration?
> 
> Hope this helps,
> 
> Dave C.
> 
> On Wed, Aug 5, 2009 at 2:11 PM, Bob Freeman<bob_freeman at hms.harvard.edu> wrote:
>> Hello all!
>> Our IT group is almost finished installing both Chado and GBrowse onto our
>> cluster and web hosting environments. Before I load any data, I was
>> wondering what programs people use for generating certain types of data. I
>> haven't been able to find any specific recommendations in any of the online
>> docs or tutorials. If I've overlooked them, my apologies.
>> Specifically, we'd like to load the following:
>> ESTs positioned against genomic scaffolds (same species)
>> BLAST? or a better program?
>> Gene models
>> These are already in GFF3 format from the model generating programs
>> Full-length mRNAs/clones (same species)
>> BLAST? or something better?
>> mRNAs from closely-related organisms for cross-species comparisons on gene
>> structure
>> ?
>> proteins from closely-related organisms for cross-species comparisons on
>> gene structure
>> ?
>> Thanks for the advice, and I welcome any additional suggestions.
>>
>> On a separate note, how do folks handle incremental updates of genome
>> assemblies? In the space of 6 months we've already moved to a 1.1 assembly.
>> Should I double the amount of analyses available? or is there a way to have
>> Chado / GBrowse remap coordinates?
>> Thanks,
>> Bob
>> -----------------------------------------------------
>> Bob Freeman, Ph.D.
>> Acorn Worm Informatics, Kirschner lab
>> Dept of Systems Biology, Alpert 524
>> Harvard Medical School
>> 200 Longwood Avenue
>> Boston, MA  02115
>> 617/432.2293, vox
>> When choosing between two evils I always take the one I've never tried
>> before. -- Mae West, Klondike Annie
>>
>>
>>
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> 
> 
>