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Pathologic GenBank File Import Weirdness- Ptools v.23

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.

    1. 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.

Pathologic GenBank File Import Weirdness- Ptools v.23

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 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.

    1. After

      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.