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Source for repeats.fa

Open qbilius opened this issue 6 months ago • 1 comments

Hi,

Thanks for your great work!

I've been struggling to identify how the repeats.fa file was created. Say I wanted to identify the source assembly for

>V-A_862
TCTACAATAGTAGAAATTTAATATATCTGTTAGAC

But running a blastn search online with default parameters fails to return any exact matches.

The article states that the sources for repeats.fa are Makarova et al. (2020) and Pinilla-Redondo et al. (2019). Since the latter focuses on Type IV systems, I looked up Makarova's data source and they seem to be solely from NCBI, thus blastn should find matching repeats, but it doesn't.

Could you perhaps clarify where these repeat sequences came from? Perhaps there is some index file, showing to the organism / assembly that, say, V-A_862 came from?

Thanks for you kind help, Jonas

qbilius avatar Aug 22 '24 17:08 qbilius