arabidopsisThalianaRefseq: Arabidopsis thaliana Refseq Genome Chromosome 3 Subset

In jackgisby/packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Arabidopsis thaliana Refseq Genome Chromosome 3 Subset

Description

The chromosome 3 reference sequence for Arabidopsis thaliana as a DNAStringSet. Can be used as a test data set, as in the associated introduction vignette. The DNA sequence between bases 10,500,000 and 14,300,000 was extracted for use in this dataset.

Usage

data(arabidopsisThalianaRefseq)

Format

A DNAStringSet object containing a DNAString for Arabidopsis thaliana's chromosome 3 sequence.

Author(s)

Jack Gisby

Source

The Arabidopsis thaliana genome was downloaded from the NCBI refseq database on 20/SEP/2019, using getGenome, and chromosome 3 was extracted. The genome may also be accessed from the NCBI ftp server: ftp://ftp.ncbi.nlm.nih.gov/genomes.

See Also

getGenome, DNAStringSet, DNAString, packSearch

Examples

data(arabidopsisThalianaRefseq)

packMatches <- packSearch(
    Biostrings::DNAString("CACTACAA"),
    arabidopsisThalianaRefseq,
    elementLength = c(300, 3500),
    tsdLength = 3
)

jackgisby/packFinder documentation built on July 19, 2022, 2:25 a.m.