Scerevisiae {BSgenome.Scerevisiae.UCSC.sacCer1}R Documentation

Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer1)

Description

Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects.

Note

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

chromFa.zip from http://hgdownload.cse.ucsc.edu/goldenPath/sacCer1/bigZips/
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

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

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

  ## 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(Scerevisiae)) {
    cat("Checking sequence", seqname, "... ")
    seq <- Scerevisiae[[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.Scerevisiae.UCSC.sacCer1 version 1.3.11 Index]