Dear,

I am interested in using MapMan for a new plant species.
I have blasted the gene models to Arabidopsis and used Arabidopsis info (BINs) to create a mapping file for my organism.
However, I assume there are better ways to create an accurate mapping file.

Are there standard procedures?


Thank you very much,

Kaat

PhD student
Centre of Microbial and Plant Genetics
KU Leuven
Belgium

Dear Kaat,

we provide an automatic mapping generation pipeline called mercator that can be accessed
via this web page: http://mapman.gabipd.org/web/guest/app/mercator
You can upload your DNA or protein sequences and the pipeline will generate a MapMan-compliant
mapping file that you can subsequently use to visualize your data in MapMan.

In case your sequence file exceeds the submission limits, please don't hesitate to contact me
again.

cheers,
Marc

Dear marc,

thank you for your fast reply.
my sequence file does exceed the submission limits (it contains all coding sequences of the predicted genes of this plant species, i.e. 44,7MB ).
what are standard procedures in this case?

thank you very much,
Kaat

Hi Kaat,

in that case you can visit http://mapman.gabipd.org/web/guest/mercator
create a new job, configure which databases you want to include in the
annotation pipeline and start the job yourself. Usually, you should receive
the results within 1-2 days (depending on cluster load).

Should you experience any problems please don't hesitate to contact me.

cheers,
Marc

hi marc,

it gives an error since my file is too big:

Error: Sequence file larger than than an overall of 30000000 nucleotides, please contact us via email to ask for processing larger amounts of data!

thank you for any suggestions,

Kaat

Hi Kaat,

that's also no problem - please use the cryptshare system to transfer your file:

https://cryptshare.mpg.de/index.php?lg=nl

simply enter my email adress lohse<at>mpimp-golm.mpg.de as the recipient
and everything should work smoothly. I will manually start the annotation job
for you and notify you as soon as it's finished.



cheers,
Marc

wauw great,
I'll do that!

Kaat