Interpretting the output

Hello Lauriebelch,

Thank you for using our tool and for reaching out with your question.

Regarding the output of the tool, the "overlap regions" section is indicating the regions that can be shared with the chromosomes. We provide more information about this on the supplementary section 18:

To annotate regions on plasmids sharing high similarity with chromosomes, we aligned complete bacterial and archaeal genomes in RefSeq to plasmids in PLSDB. Based on the alignment, we defined the high-similarity region as the alignment where the length was greater than 300 bp, and the identity was greater than 90%. During testing, we will parse the alignment results and provide the alignment length and the start and end positions of the query contigs aligned to the high-similarity regions in the output file. Users can use the alignment results to determine whether the identified plasmids are likely to be false positives.

For example:

I have some contigs that report one overlap region e.g. "overlap regions: 87950-124985"

For this query contig, the region from 87950 to 124985 can be also aligned with chromosome.

I have some contigs that report multiple overlap regions e.g. "overlap regions: 33029-36332 6979-33028"

"overlap regions: 33029-36332 6979-33028" should be "overlap regions: 6979-33029", I will fix it.

I have some contigs that report no overlap regions e.g. "overlap regions: "

For this query contig, it doesn't contain any region shared with chromosomes in the current database.

I hope this helps, please let me know if you have any further questions.

Best regards, Xubo Tang

HubertTang / PLASMe

Interpretting the output #1