arabidopsisThalianaRefseq {packFinder} | R Documentation

## 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
    )

[Package packFinder version 1.2.0 Index]