There is an interesting function at NCBI website called primer-blast (http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-13-134). This function infers the expected amplicons coordinates when a primer pair sequences are tested against a genomic sequence.

I would like to know if there is some function with similar objective in the Bioconductor project. Let´s say that I am a code like that:

### Loading genomic sequence
library(Biostrings)
g = readDNAStringSet("genomicseq.fa") 

### Loading primer GRanges position
library(GenomicRanges)
gr <- 'chr start end strand
       chr1 10  30  +
       chr1 100 120 -'
gr <- read.table(text=gr, header=T)
gr <- makeGRangesFromDataFrame(gr, start.field="start", end.field="end", strand="strand")

What could I do with "g" and "gr" objects to find possible amplicons here?
 

Hi,

It's not clear to me whether you want to design primers or if you already have a set of primers and want to match them against a genome to find the theoretical locations of the amplicons. If the fomer, check out the DECIPHER package which provides tools for primer design:

    http://bioconductor.org/packages/DECIPHER

If the latter, please have a look at matchProbePair() in the Biostrings package. See ?matchProbePair (after doing library(Biostrings)) for more information.

H.

PS: FWIW you can create your GRanges object gr with just:

GRanges(c("chr1:10-30:+", "chr1:100-120:-"))