What Package would you suggest to represent sequence alteration events?

Specific Domains Biology, Health, and Medicine
1

Hi

I am looking for a package that would allow me to represent changes to a sequence. Is there something like that around? I looked at GenomeGraph and PopGen (and PopGenSim) but their documentation is quite sparse to understand what is actually going on.

Any suggestions?

Thank you

Marco

2

Maybe this is what your looking for?
https://biojulia.net/Bio.jl/latest/man/seq/sequences/bioseq/

I haven’t done any bioinformatics in Julia yet. but I likely will in the near future, so I’d be glad to hear what packages you use in the end.

3

It depends which types of alteration you’re speaking about, but usually mutations are represented by a genomic position, the reference sequence at that position, and the alternative sequence, plus some other metadata. The standard format for that is VCF, but if you don’t need to read/write vcf files you could use a named tuple or even a dataframe.

1 Like
4

Definitely not - the Bio.jl monorepo is deprecated. That module is now BioSequences.jl, but you may also want BioAlignments.jl?

5

Thanks!!

Googling Julia can be a bit of a minefield. Took me a while to figure out that I was often reading the docs of older versions of packages etc.

2 Likes
6

Yeah, that’s a common experience :persevere:. There have been efforts/intentions to throw warnings on older docs versions, though I don’t know how far along they are.

7

Thank you. Yep. Roundtripping VCFs and BCFs will be useful, but that is not quite what I am after. I want to create a simulator for evolutionary processes.

I decided to cook up something as a learning experience.

I will kee you posted.

8

I did get that feeling. :expressionless: