Protein sequence from a gene fusion?

Question

[bioinf_sci]

I need to get a protein sequence from a gene fusion. For example, say you have a gene fusion at chr1:[position] and chr2:[position]. From these genomic coordinates, how can I get the resulting protein sequence that spans this fusion? It can be just several peptides.

Ultimately, I need to translate the gene sequence at each breakpoint to the resulting protein sequence. What tool can I use for this?

I primarily work in R, so any libraries that can accomplish this would be helpful. Thank you!

Answer 1

[benformatics]

If you already have the coordinates in GRanges format and a FASTA genome handy then you should be able to do everything you need with https://bioconductor.org/packages/release/bioc/html/Biostrings.html