refseq_CDSseq: Extract the CDS nucleotide sequence into a Biostrings object

In refseqR: Common Computational Operations Working with RefSeq Entries (GenBank)

Extract the CDS nucleotide sequence into a Biostrings object

Description

refseq_CDSseq() Parses a single/multiple transcript accessions (RefSeq format) and extract the CDS nucleotide sequences into a DNAStringSet object.

Depending on the function, available accessions in refseqR include RefSeq models with the prefixes XM_ (mRNA), XR_ (non-coding RNA), and XP_ (protein), as well as subsequently curated RefSeq records with NM_, NR_, or NP_ accession prefixes.

Usage

refseq_CDSseq(transcript)

Arguments

transcript

A character string of the single/multiple transcript id.

Value

An object of DNAStringSet class.

Author(s)

Jose V. Die

See Also

refseq_CDScoords

Examples

transcript <-  c("XM_004487701", "XM_004488493", "XM_004501904")
my_cds <- refseq_CDSseq(transcript)
# Now, the `DNAStringSet` can easily used to make a fasta file :
# writeXStringSet(x= my_cds, filepath = "cds_result")

refseqR documentation built on Oct. 30, 2024, 1:06 a.m.