Hi guys,

I am working on transcriptomics study (RNA seq) of ryegrass (lolium prerenne) under water deficit stress. And I am really impressed by the overview of pathways and high resolution picture output features of MapMan, and want to use it in my data analysis. Is it possible to extend MapMan to my study? As there is no mapping file etc of ryegrass in Mapman database. Or should I generate my own mapping file? And how to do it? I have read the Manual several times, but did not figure out how to do so.

Looking forward to seeing your answer or suggestions.

Best,

YF

Hi yanfei zhou,

to-date, we don't have a ryegrass mapping in the public MapManStore. We can, however, create
such a mapping using the mercator pipeline (http://mapman.gabipd.org/web/guest/app/mercator)
if you can provide the protein or nucleotide sequences in FASTA format.

You can send the sequences using our secure transfer system: https://cryptshare.mpg.de/index.php?lg=en

best greetings,
Marc

Hi Marc,

Thanks for your suggestion. By the sequences, do you mean the whole EST library or only genes differently expressed?

best regards,

YF

Hi,

both would be possible - i would, however, suggest that you send the whole set - so you will get
functional annotations for each (putative) transcript you have.

cheers,
Marc

Hi Marc,

That sounds good. Can you let me know your email address please? THe MPI cryptshare requests it.


Cheers,

YF

Ah sorry - i had forgotten to post it: lohse_at_mpimp-golm.mpg.de

cheers,
Marc

Hi Marc,

I have uploaded the file on cryptshare. Please let me know through email if you have got the notification message.


Cheers,

YF