morganmcg1

jph00

(from @philippbayer)

1. Gene function prediction - given a predicted protein or gene sequence, what is the function?

The classic approach is to use something like BLAST to compare with known sequences, but this has many drawbacks. For starters, in plants the databases lean very heavily towards Arabidopsis thaliana, not more common plants such as maize or wheat.

People do get around this by looking for protein domains (Hidden Markov Models) but that doesn't go very far either, you have to describe domains first, and many are very generic. Can we classify protein/gene sequence using RNN/CNNs? Here's an example where someone tried

richardxiong

Current configuration works for my GPU and notebook, hope it helps

It is based on (a different configuration): https://gist.github.com/jganzabal/8e59e3b0f59642dd0b5f2e4de03c7687

and on (multiple choices for different GPU drivers): https://www.tonymacx86.com/threads/nvidia-releases-alternate-graphics-drivers-for-macos-sierra-10-12-6-378-05-05-25.227494/

Hardware

• MacBook Pro (Retina, 13-inch, Early 2015)

horiacristescu

Make a bookmarklet with this code:

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