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Russel88 / CRISPRCasTyper

CCTyper: Automatic detection and subtyping of CRISPR-Cas operons
https://typer.crispr.dk
MIT License
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Question about spacer direction #19

Closed Dfvandenberg closed 2 years ago

Dfvandenberg commented 2 years ago

Dear Russel,

are the spacers correction for their orientation like CRISPRDetect/CRISPRDirection does?

With kind regards, Daan

Russel88 commented 2 years ago

Dear Daan,

This is currently not implemented, but we are working on adding this as an extension. However, I will also point you to this paper (https://doi.org/10.3389/fmicb.2019.02054), which suggests that the orientation most of the time matches with the orientation of the associated cas genes. In the cctyper output you can find the direction of the interference and adaptation modules. However, this criteria can obviously not be used for orphan arrays.

Best, Jakob

Dfvandenberg commented 2 years ago

Dear Jakob,

thank you for your response! I will read it.

with kind regards, Daan