Visualising SeqRecords with compound locations
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Entering edit mode
3 months ago

Hi All,

I've written some gbk files from SeqRecords containing SeqFeatures with compound locations. I'm currently trying to visualise the gbks with SnapGene, but it looks like it struggles to visualise these compound locations - some of the feature bars look like they are disappearing halfway through some sub-location parts (rather than between sub-location parts). I'm guessing this is a snapgene-specific issue - I have checked that the compound locations are as expected both in the SeqRecord and in the GBK snapgene visualisation, and they are. It's just the snapgene visualisation that looks wrong.

I've tried some other viewers, but they tend to represent the compound locations as sets of separate features with locations corresponding to the compound location parts. This happens with benchling, and https://edinburgh-genome-foundry.github.io/DnaFeaturesViewer/tips.html - these are the two ones that I've tried so far.

If anyone has any experience with this very niche issue, have you got any tips? Alternatively, have you got any open source gbk viewers to recommend?

Thanks!

Edit - the reason why I want to get snapgene working is because the compound locations are represented on a single track for the feature, whereas the viewers that represent the compound locations as separate features don't keep the features together. For compound features with lots of parts, this can complicate seeing where the feature components are located.

genbank snapgene benchling biopython • 111 views
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