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Pathologic GenBank File Import Weirdness- Ptools v.23

asked 2019-05-09 10:58:10 -0500

gpharhay gravatar image

updated 2019-05-09 11:32:16 -0500

These glitches concern ptools v 23.

I'm using Pathologic to convert GenBank .gbk files into PGDBs. I noticed a few problems detailed below.

1.In both desktop and web versions of ptools, the gene frames do not show the PGDB accessions, although the NCBI locus_tags are visible. That's a big problem for those of us using the PGDB accessions in downstream compute processes.

2.After running an initial Pathologic .gbk import (create overview checked at pathologic import step) followed by a save, the genome overview shows a bunch of black orfs, no color. Zooming in within the overview shows a white boxes, no color. The only way I could get the overview to look "normal" was to run hole filling. Rescoring pathways and /or Predict Transcription Units didn't correct the overview problem.

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answered 2019-05-09 12:14:25 -0500

Suzanne Paley gravatar image

Are you sure the locus_tags aren't also the PGDB accessions? I think we're trying to do that now, where possible, to limit proliferation of ids, and we won't bother to list the same accession twice. In the desktop software, you can right-click on the gene name and select Show->Show frame name to print its PGDB id in the console panel, if you're not sure what it is.

I can't speak to the genome overview question -- hopefully someone else can address that.

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Oh, OK -- Locus_tag is the frame name & PGDB id. I was unaware of that change. That change makes a lot of sense to me.

gpharhay gravatar imagegpharhay ( 2019-05-09 12:19:43 -0500 )edit

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Asked: 2019-05-09 10:58:10 -0500

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Last updated: May 09 '19