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linsalrob / ProphagePredictionComparisons

Comparisons of multiple different prophage predictions
MIT License
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Some contig accession numbers in the Supplementary Tables seem to be incorrect? #14

Open leannmlindsey opened 6 months ago

leannmlindsey commented 6 months ago

I tried to download all of the genomes using the "Contig accession" column in the supplementary table and these are the ones that were not recognized:

411479.31.con.0020 1351.557.con.0001 1280.10152.con.0001

Searching https://www.ncbi.nlm.nih.gov/ also produces no results.

Do you know where you got these?

Thank you

pdec commented 6 months ago

These are sequence IDs from BV-BRC (previously PATRICBRC) service. In particular, 411479.31 is Genome ID, while 411479.31.con.0020 is Sequence ID of one of its contigs.

You can find genomes using Genome Browser and then view a particular one by selecting it and choosing a "Genome" icon in the menu on the right, or view it directly like that: https://www.bv-brc.org/view/Genome/411479.31

Also, you can explore BV-BRC CLI to access its resources: https://www.bv-brc.org/docs/cli_tutorial/index.html Then, you can use these IDs to fetch data for particular records.

I hope it helps.

leannmlindsey commented 6 months ago

Thank you.