Questions on handling circular genomes

Pedro Fernandez

• March 21, 2025 15:07

Hello,

I'm currently developing a plugin for annotating bacteriophage genomes, and I'm encountering some issues with circular genomes. When processing circular genomes, my plugin crashes, but it works fine if I linearize the sequence. I'm particularly curious about the following:

1. Circular Genome Handling:
   Is there any documentation or guidance on how Geneious handles circular genomes, particularly regarding the SequenceDocument class? I'm currently converting the dna doc to a string and scanning through that but I think that is where my issue is arising.  Additionally, I'm interested in understanding how the SequenceAnnotationGenerator should add an annotation that begins at the "end" of a circular sequence and wraps around to the beginning.

2. Marker Scanning Efficiency:
   My current approach involves scanning through the genome twice and deleting any repeats to find specific markers. Is there a more efficient or recommended method for handling this task in circular genomes?

Any insight or documentation you could provide would be greatly appreciated. Thank you!

1

• Official comment

  

  Matt Kearse

  • March 26, 2025 04:07

  Hi Pedro,

  Sorry for the slow reply!

  1. SequenceDocument.isCircular() has a link to SequenceAnnotationInterval.getFrom() which describes how annotation intervals should be created on circular sequences.

  2. It really depends on the details of your algorithm. Some of our algorithms will concatenate a sequence with itself and treat it like it's linear so that the region spanning the origin is continuous. And then, depending on the algorithm, you may need to normalize the position of results and remove duplicates.

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