Two queries: i. What is the package in Bioconductor where the position of a SNP can be specified to get its flanking sequences? ii. What is the way to highlight or put brackets around a nucleotide at a specific position in a DNA String Set? Thanks in advance. Prodhan

For the first question, you will use the GenomicRanges package and a package or other source with relevant reference genome, e.g.,

library(GenomicRanges)
library("BSgenome.Hsapiens.UCSC.hg38")

Create or input (e.g., with VariantExperiment::readVCF() or rtracklayer::import()) a GRanges object representing the SNPs

snps <- GRanges(
    c("chr1:1000000", "chr2:20000000", "chr3:30000000")
)

Use flank() to define the regions of interest

flanks <- flank(snps, 100)

Retrieve the flanking sequences from the relevant genome

getSeq(BSgenome.Hsapiens.UCSC.hg38, flanks)

Packages with whole-genome sequences start with "BSgenome", so use

BiocManager::available("BSgenome")

to see available genomes, followed by BiocManager::install(full_package_name) to install it.

Alternatively, search the AnnotationHub for whole genome sequences, especially from Ensembl

> library(AnnotationHub)
> hub = AnnotationHub()
> query(hub, c("ailMel1", "2bit", "release-96"))
AnnotationHub with 4 records
# snapshotDate(): 2019-07-10
# $dataprovider: Ensembl
# $species: Ailuropoda melanoleuca
# $rdataclass: TwoBitFile
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH69768"]]'

            title
  AH69768 | Ailuropoda_melanoleuca.ailMel1.cdna.all.2bit
  AH69769 | Ailuropoda_melanoleuca.ailMel1.dna_rm.toplevel.2bit
  AH69770 | Ailuropoda_melanoleuca.ailMel1.dna_sm.toplevel.2bit
  AH69771 | Ailuropoda_melanoleuca.ailMel1.ncrna.2bit

and use that

seq = hub[["AH69769"]]
getSeq(seq, flanks)