secretome P error

Question

[1234anjalianjali1234]

hellow,

I am doing secretome analysis of a fungus, i am trying to find non-classical secreted proteins for which i have to run sectretome P. when i am trying to run the software with its given data, it is giving error:

Merging featuresError: id FGF1_HUMAN is missing features ( prop_vect_5d psort_vect tmhmm_5d )

Error: id ATRX_HUMAN is missing features ( prop_vect_5d psort_vect tmhmm_5d )
Error: id FGF4_HUMAN is missing features ( prop_vect_5d psort_vect tmhmm_5d )
Unable to create secretome

I have no idea what is going wrong.

ThankYou

Answer 1

[Jean-Karim Heriche]

Missing features could indicate that some features couldn't be computed. One possible reason is that you didn't install software required to compute them. See the docs for secretomeP.

One another note, it seems that using secretome P (that has been trained with mammalian proteins) for non-mammalian proteins has issues as explained in this article on using it for plants. The main point is:

Applying SecretomeP to plant protein data implies a chain of assumptions that the features shared between mammalian CSPs and LSPs are conserved and also shared with plant CSPs and LSPs. Our results show that these assumptions do not hold, and that observations of the accuracy in the literature are not supported.