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HubertTang / PLASMe

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The question regarding your DB database #12

Open zzzfire opened 5 months ago

zzzfire commented 5 months ago

Hello author, regarding your DB database, I would like to know how the files plas_chrom_thres.csv, plas_overlap.csv, and plsdb_Mar30.clusters.p2a were processed and obtained?

HubertTang commented 5 months ago

Hi zzzfire,

Regarding your questions, you can refer to the paper as well as the Supplementary:

  1. plas_chrom_thres.csv: Supplementary S3 Thresholds of PC tokens.
  2. plas_overlap.csv: Supplementary S18 Annotating the high-similarity regions on the plasmids.
  3. plsdb_Mar30.clusters.p2a: Article - Materials and methods - Protein clusters (PC). After obtaining the PC, we mapped the protein ID to its corresponding PC index to obtain the p2a file.

Here is the link to the article and Supplementary: https://doi.org/10.1093/nar/gkad578

zzzfire commented 4 months ago

Thank you for your reply, I would like to inquire about the "Thresholds of PC tokens" section in the Supplementary. I am wondering what bioinformatics software you used to generate the thresholds of PC tokens, or if you could share the relevant code for generating the Thresholds.