Hi Kai -
So I no longer work on apollo but I used to - the current apollo
developer is Ed Lee. He is doing some excellent work with apollo but I
dont think he has dived into the synteny viewer yet (as theres a million
other things to be done of course - and hes done a lot!)
So I used to work on the synteny viewer, but I worked on the game
synteny viewer not the gff synteny viewer which have their differences.
The gff synteny viewer was worked on at the sanger center by (I believe)
Vivek Iyer and/or Steve Searle(?) - Vivek doesnt work on apollo anymore
and i dont think hes on this list. Steve occasionally works on apollo
and I think he is on this list.
Anyways, I think gff synteny might not be working (where game synteny
does), but if its not working I dont think it will take much to bring it
back to life.
In doc/html/synteny.html are some docs about it - for gff synteny its at
the bottom of the doc(most of the doc is about yet another synteny
adapter - ensembl) .
For gff synteny you need to explicitly load the link file in addition to
the 2 species/annotation files. (in other synteny adapters you dont have
to load a separate link file)
The doc mentions a link file data/links.gff which doesnt seem to be in
apollo cvs anymore.
However I did notice 3 files in the apollo data directory which Im sure
are for synteny gff:
ENSMUST00000037953.gff
ENST00000225388_ENSMUST00000037953.gff
ENST00000225388.gff
So these are probably the files to try out and see if apollo even works
for synteny gff, the 2nd one is the link file. It will need to be
configured according to the doc page above. And if it doesnt work then
obviously it needs a little dusting off & debugging.
Hope this helps - Mark
[EMAIL PROTECTED] wrote:
Dear all:
I am a new user to apollo, I wonder if currently the synteny view is work
(v1.9.0) for GFF format??? I tried the game xml seems work, but it is too
complicate for me now. can any one provide a sample data set (species1.gff
species2.gff and SPECIES1-SPECIES2-compare.gff )or provide some information
how cross-speecies link gff file should write(I can not find any sample file
with the distribution).
thanks and best wishes
Kai Ying
Interdepartmental Genetics Program
Iowa State University
2043 Roy J. Carver Co-Laboratory
ISU, Ames IA 50010
Email: [EMAIL PROTECTED]
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