Forum:Tools and data for plant proteins

Question

[Shide]

Hi All,

Hope you are well.

I'm coming here to get know-how from experts here.

I'm currently studying the plant protein sequences and the use of digital for identification. Basically, the goal would be to have a peptide sequence and find a similar one in the vegetal world.

A few questions are raising :

• Are there any relevant entities/ platforms focusing on those plant based identification ? if yes, which one ? As of today i found companies that are producing new flavours ( Mccormick and IBM with the one platorm)

• I think what is the most important is to have a database big enough to cover the vegetal span. Are there existing database that would be representative ? I found for example "nr protein database"

I'm looking forward to read your comments, thank you in advance

Best
Shide

[lieven.sterck]

nr is certainly an option and that will be even the most comprehensive one but it also contains proteins from all known organisms ( so not ONLY plants) you can subselect from it though eg. using taxonomy filtering with the tag "viridiplantae" .

One other plant focussed resource that comes to mind is for instance PLAZA, ENSEMBL-plants ... those are focussed on plants but might not be as comprehensive as nr .