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Shamir-Lab / PlasClass

A tool to classify sequences of plasmid or chromosomal origin. A paper describing this tool is available at: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007781
MIT License
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Highly scoring plasmid in an organism where No plasmid is reported in Literature #14

Closed Rohit-Satyam closed 2 years ago

Rohit-Satyam commented 2 years ago

Dear Developer

I was trying to use PlasClass to score my contig as plasmid or not. Since the organism (The entire genus) is given to me Tenacibaculum_dicentrarchi_gca_900239345 does not have plasmid your tool still shows it contains plasmid:

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Tenacibaculum_dicentrarchi_gca_900239345 | TDCHD05_Contig_17 | 0.954729 | >TDCHD05_Contig_17 dna:supercontig supercontig:TdChD05_V1:TDCHD05_Contig_17:1:14961:1 REF | 14961 -- | -- | -- | -- | --

With such a high score and contig length is also high. How do I explain such discrepancy?

dpellow commented 2 years ago

I don't fully understand the question. What are you trying to classify, did you assemble a genome or metagenome from reads? Plasmids can move between bacteria and may be found in different strains or individuals, the fact that a specific draft genome of your species didn't have plasmids doesn't mean that your sample won't.