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CCB-SB / plsdb

PLSDB pipeline to collect bacterial plasmids from NCBI
https://ccb-microbe.cs.uni-saarland.de/plsdb/
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Include archaeal plasmids #14

Open apcamargo opened 2 years ago

apcamargo commented 2 years ago

PLSDB currently hosts only bacterial plasmids. WOuld it be within the project's scope to also add plasmids of Archaea?

Xethic commented 2 years ago

Hi, we are currently reviewing this option and keep you in the loop via this thread.

Best

SDmetagenomics commented 2 years ago

Yes we would very much like to see this implemented. I have done a rudimentary version using the same search string you guys used slightly modified:

biomol_genomic[PROP] AND plasmid[filter] NOT complete cds[Title] NOT gene[Title] NOT genes[Title] NOT contig[Title] NOT scaffold[Title] NOT whole genome map[Title] NOT partial sequence[Title] NOT partial plasmid[Title] NOT locus[Title] NOT region[Title] NOT fragment[Title] NOT integron[Title] NOT transposon[Title] NOT insertion sequence[Title] NOT insertion element[Title] NOT phage[Title] NOT operon[Title] AND archaea[filter]

Made non-redundant by mash clustering with dist = 0

Seems like this would be an excellent addition to the next update!