Genbank feature location spans zero

James Morris

• March 01, 2021 16:33

Hello,

We have a problem with a genbank file generated in geneious that contains a feature that spans zero.

We are using the biojava genbank parser and we get the following error trying to read in a geneious genbank file:

Caused by: java.lang.IllegalStateException: Start (11784) is greater than end (4); this is an incorrect format

I have a couple of questions about this I hope you can help me with:

Is the format that Geneious uses for features that cross zero supported by the genbank format? Thus it is the biojava parser that is not correct.

Or is the format for features that cross zero not fully specified, meaning the Geneious implementation is valid but just not supported by biojava?

Many thanks,
James

 

0

• Official comment

  

  Jonas Kuhn

  • March 02, 2021 04:31

  Hi James,
  
  Thanks for bringing that to our attention.
  
  To the best of my knowledge the latter is the case:
  There is no satisfyingly clear specification how a feature that spans the origin should be declared in a Genbank file.
  The implementation that Geneious uses is supported by some programs (e.g. SnapGene), but some others (e.g. biojava) don't seem to support it.

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