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wilkelab / Opfi

A Python package for discovery, annotation, and analysis of gene clusters in genomics or metagenomics data sets.
https://opfi.readthedocs.io/
MIT License
21 stars 5 forks source link

adding transposon gene location in operon_analyzer #213

Open Jigyasa3 opened 1 year ago

Jigyasa3 commented 1 year ago

Hi,

Thank you for creating a great platform to examine the CRISPR-Cas transposon systems bioinformatically! I was able to follow along the tutorial to find CRISPR and Cas proteins in the genome of interest and classify them into CAST systems based on their presence and distance in the genome. I wanted to ask how were the transposons annotated in the paper? How were the transposon genetic location with respect to cas proteins examined in the operon_analyzer script?

Looking forward to your reply, Jigyasa

jimrybarski commented 1 year ago

I'm a little unsure what you're asking for. The parameters for the search are in the methods section - is there something specific you can't find? If you're asking how we made the figures, they were initially visualized with DNA features viewer and we made the final figures in Adobe Illustrator manually.

Jigyasa3 commented 1 year ago

Hey @jimrybarski ,

Thank you for replying! I wanted to know more about the BLAST filters used. What was the percent identity, sequence coverage and e.value cutoffs? Were default values used or specific filters?

Regards, Jigyasa