Hi ,

Is there a way to use MapMan with unknown plant species (melon)? I only have GO and EC number of blast search assigned for each gene identifier ID.

For example

M1 GO:1:GO2
M1 EC1:EC2

If yes - could you please let me know where I can find documentation how to do that?

Best

Hi Eli,

if you have the nucleotide sequences of the transcripts you would like to have a mapping
for you can use the mercator tool (http://mapman.gabipd.org/web/guest/app/mercator) to
automatically create a MapMan mapping of them.

If your dataset is too large for submission via the web interface, please don't hesitate to
contact me and i will submit the data for you.

cheers,
Marc

Hi Marc,

thanks for your answer.

Yes we do have the nucleotidesof the transcripts (not the CDS) derived from RNA-seq assembly.
Is it possible to start from the transcript (not CDS) and to go over the analysis of mapman including the mapping, images
the statistical analysis of metabolomics pathways of BINs etc ...

Thanks, Eli

Hi Eli,

yes, it it possible to use the putative transcripts assembled from RNA-Seq data. That said,
however, the percentage of sequences that can be assigned to a functional bin is usually
lower than when using full CDS sequences. The reason for this is that primary RNA-Seq
transcriptome assemblies still contain a lot of partial and also misassembled sequences.

If you want to supply the sequences via a safe, encrypted data transfer service (in case it
is confidential data), please use the cryptshare system: https://cryptshare.mpg.de/?lg=en

To provide the data simply use my email adress as the recipient: lohse@mpimp-golm.mpg.de

cheers,
Marc