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ccdmb / predector

Effector prediction pipeline based on protein properties.
Apache License 2.0
11 stars 7 forks source link

FEATURE REQUEST: secretomeP #45

Closed xizhesun closed 3 years ago

xizhesun commented 3 years ago

What kind of feature are you proposing? secretomeP analysis, which related to the Non-classical secreted proteins. It could be a reference for the effector candidates.

darcyabjones commented 3 years ago

Hi Xizhe,

Previously we've found that secretomeP isn't precise enough to be useful for this task. It's fallen out of favour with most of the bioinformatician that I know.

E.g. https://www.frontiersin.org/articles/10.3389/fpls.2015.01168/full https://www.frontiersin.org/articles/10.3389/fpls.2016.01451/full

The other aspect is the installation. I remember having to install it years ago, and there is a dependency that can only be obtained by emailing the author directly. It took a week for them to email me the installer.

Doesn't seem worth the trouble.

xizhesun commented 3 years ago

yeah, I agree with you! It's really hard for the installation. I also install one year ago. I successfully run it on a ubuntu machine. but failed on the WSL of my laptop.

darcyabjones commented 3 years ago

Thanks