Athaliana {BSgenome.Athaliana.TAIR.01222004} | R Documentation

## Arabidopsis thaliana full genome (TAIR version from January 22, 2004)

### Description

Arabidopsis thaliana full genome as provided by TAIR (snapshot from January 22, 2004) and stored in Biostrings objects.

### Note

This BSgenome data package was made from the following source data files:

    ATH1_chr1.1con.01222004
    ATH1_chr2.1con.01222004
    ATH1_chr3.1con.01222004
    ATH1_chr4.1con.01222004
    ATH1_chr5.1con.01222004
    mitochondrial_genomic_sequence
    ATH1_chloroplast.1con.01072002
    from ftp://ftp.arabidopsis.org/home/tair/Sequences/whole_chromosomes/OLD/

See `?BSgenomeForge` and the BSgenomeForge vignette (`vignette("BSgenomeForge")`) in the BSgenome software package for how to make a BSgenome data package.

### Author(s)

H. Pages

### See Also

BSgenome-class, DNAString-class, `available.genomes`, BSgenomeForge

### Examples

    Athaliana
    seqlengths(Athaliana)
    Athaliana$chr1  # same as Athaliana[["chr1"]]

    if ("AGAPS" %in% masknames(Athaliana)) {

      ## Check that the assembly gaps contain only Ns:
      checkOnlyNsInGaps <- function(seq)
      {
        ## Replace all masks by the inverted AGAPS mask
        masks(seq) <- gaps(masks(seq)["AGAPS"])
        af <- alphabetFrequency(seq)
        found_letters <- names(af)[af != 0]
        if (any(found_letters != "N"))
            stop("assembly gaps contain more than just Ns")
      }

      ## A message will be printed each time a sequence is removed
      ## from the cache:
      options(verbose=TRUE)

      for (seqname in seqnames(Athaliana)) {
        cat("Checking sequence", seqname, "... ")
        seq <- Athaliana[[seqname]]
        checkOnlyNsInGaps(seq)
        cat("OK\n")
      }
    }

    ## See the GenomeSearching vignette in the BSgenome software
    ## package for some examples of genome-wide motif searching using
    ## Biostrings and the BSgenome data packages:
    if (interactive())
        vignette("GenomeSearching", package="BSgenome")

[Package BSgenome.Athaliana.TAIR.01222004 version 1.3.11 Index]