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Creating a 5 or 10-fold cross validation based on sequence similarity of proteins

Hi there,

As the post title states I am trying to find an approach to construct a 5 or 10 fold cross validation dataset, applied to all of the currently available human proteins in Swiss-Prot (20.421 proteins).
Ideally, in each of the folds there should be the most similar proteins in terms of their sequence identity.
What can be a way to divide the proteins into the respective cross validation sets based on similarity?

proteins cross-validation machine-learnng
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updated by trent • trent • written by rafi.zon • rafi.zon

1 answer

I wrote how I did this with CD Hit here, hopefully it's helpful: https://www.trenthauck.com/cd-hit-cross-validation

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written by trent • trent

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