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simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
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linear & circular Labeling chaos In the resulting Genebank file #76

Open fangzhou233 opened 4 years ago

fangzhou233 commented 4 years ago

Hi Simroux: I really appreciated this pipeline you contributed to the viral study. This is a question. In the predictions, the comments in the genebank file were inconsistent with the information in the contig names. Which one should I believe?

Thank you very much！ Zhou Fang

LOCUS VIRSorter_NM_tailings_Scaff622018-circular_gene_14_gene_116-6603-71618-cat_5 65015 bp dna linear ENV 03/26/20

DEFINITION Putative phage sequence (category 5), predicted by PhageSorter ACCESSION VIRSorter_NM_tailings_Scaff622018-circular_gene_14_gene_116-6603-71618-cat_5 KEYWORDS . FEATURES Location/Qualifiers source 1..65015 /organism="Putative phage sequence (category 5), predicted by PhageSorter" gene 50..760 /gene="gene_14"

simroux commented 4 years ago

Hi ! Not sure what's inconsistent here. The contig itself (NM_tailings_Scaff622018) is detected as circular (i.e. it has direct terminal repeats). Then within this contig, a specific region (6603 to 71618) is flagged by VirSorter as likely viral. The GenBank file itself should contain only this predicted viral region (6603 to 71618), so is technically linear.

Not sure if it answer the question ?

Best, Simon