Hi Dear admins

The mapping files of soybean I believe are from old gene models (Phytozome v1.0), I am using new gene models (v1.1) with 54175 genes and 73320 transcripts( including alternative splice variants). I am wondering if there is any updated soybean mapping file with new bins have been created?

Thanks

You could run it through Mercator. There was not too much difference and both versions looked relatively immature.

Best Wishes,
Björn

I am sorry, I am quite new with mapman. what is Mercator?
New and old versions have only 38274 IDs in common.
Old one had ~48000 (~55000 transcripts) gene models whereas new have 54174 (73320 transcripts).

Hi Waseem,

if you send me a link to the FASTA file you'd like me to generate a mapping
for i will start a mercator job manually and notify you once it's done.

cheers,
Marc

ftp://ftp.jgi-psf.org/pub/compgen/phytozome/v9.0/Gmax/annotation/

You might use Gmax_189_protein.fa.gz

Hi ,

we are currently working on generating mappings for all current (v9.0)
phytozome proteomes, which includes the soy bean proteome you
requested. As soon as we are done we will make all of them available
via the MapManStore repository (http://mapman.gabipd.org/web/guest/mapmanstore).

In case you need the mapping very urgently i can send you a preliminary
version upon request.

Best greetings,
Marc