Purpose of Seqinfo Circularity Attribute in GenomicRanges Objects

Question

[jon.klonowski]

What is the purpose and functional purpose of the Seqinfo object circularity attribute in GenomicRanges objects?

I know that MT genes are circular, and you can use this attribute to label them as such, but why would I do that?

I read the manual for these objects, but little to no clarification about this attribute is given:

https://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/GenomicRanges/html/GRanges-class.html

https://web.mit.edu/~r/current/arch/i386_linux26/lib/R/library/GenomeInfoDb/html/Seqinfo-class.html

Thank you!

[rpolicastro]

In genomics the genome is usually represented as a linear string of bases. This is somewhat problematic for circular genomes because you can have annotated features or NGS reads that partially overlap both the beginning and end of this linear string, since in reality they are just one continuous sequence. If there was no indicator of circularity you would have no way to programmatically check whether these features or reads are legitimate or just some error in annotation or alignment.

Answer 1

[seidel]

For any chromosome, it's useful to have an indicator of circularity so you can determine programmatically what to do when reads or features map across the ends. For linear chromosomes it doesn't make sense to have features extending beyond the boundaries, but for circular chromosomes you can still do the base pair math, if you know they're circular.

[jon.klonowski]

Ok thank you! Otherwise it does not modify the sequences that are under the seqname with that flag, yes?

I am manipulating sequences using GRanges (creating alternative proteins and such) so I want to make sure it doesn't impact the sequences / functionality of these sequences.

Thanks again!

[seidel]

It doesn't modify the sequence. It is simply a place to store or reference the attribute. However, I would probably test the behavior of a given function, to see if it will take circularity into account. For instance, if you pick a base near then end, then resize() it to something which would run off the end. GRanges with A linear chromosome would return a warning and the suggestion to trim the coordinates. I'm not certain how GRanges deals with running off the ends of circular chromosomes (thus I would test).