blastn in R using as a subject sequence a personally sequenced genome

Question

[simone.moro.2]

Hi everybody,

do you know if it is possible to use blastn in R to align genes sequences (query sequence) to a personally sequenced bacterial genome (subject sequence).

Thank you.

Answer 1

[Neilfws]

You can call external programs from within R, so I suppose you could call blastn. I'd think it was as easy to run blastn by itself, specify the delimited output option and read that into R.