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Matteo-Ciciani / PAMpredict

A python package to predict CRISPR-Cas PAMs
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Requirements regarding spacers' direction #7

Open pengxi1209 opened 1 month ago

pengxi1209 commented 1 month ago

I want to know when the predicted array is on the negative chain, should the spacer sequence in the input file spacer.fna be the original spacer sequence on the negative chain, or the sequence on the positive chain that is opposite to it and complementary to it?

Matteo-Ciciani commented 1 month ago

Hi, it should work regardless of the of the spacer orientation you provide in the spacer.fna file. If the expected PAM position with respect to the spacers is downstream (--pam_position DOWNSTREAM) and you provide spacers in the reverse orientation, the PAM will be initially predicted upstream with respect to the spacers and then reverse complemented to match the expected position (this is the result you find in the output). This also allows to infer the array orientation (expected PAM downstream but predicted PAM is upstream --> array is on the reverse strand), you can find this in the PAM_prediction.txt file.