pathway analysis in plants

Question

[Ric]

Hi, We have de-novo assembled a non-model plant genome, and we also annotated it by ourselves. Which tools are recommended to do pathway analysis?

Thank you in advance,

Answer 1

[Antonio R. Franco]

If you have a nice KEGG annotation (get KO tags using blastKoala) and complement the annotations with several other different applications you can run KEGG Mapper, although not all pathways are included and it is almost certain that many genes will eventually not be annotated. There are R packages that use KEGG to do the same task

Answer 2

[Tm]

You can use KAAS online server for identification of KEGG pathway in which each gene participate.