Dmelanogaster {BSgenome.Dmelanogaster.UCSC.dm3} | R Documentation

## Drosophila melanogaster full genome (UCSC version dm3)

### Description

Drosophila melanogaster full genome as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects.

### Note

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

    sequences: chromFa.tar.gz, upstream1000.fa.gz, upstream2000.fa.gz, upstream5000.fa.gz
    from http://hgdownload.cse.ucsc.edu/goldenPath/dm3/bigZips/
    masks: all the chr*_gap.txt.gz files from ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/database/
    + chromOut.tar.gz and chromTrf.tar.gz from http://hgdownload.cse.ucsc.edu/goldenPath/dm3/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

    Dmelanogaster
    seqlengths(Dmelanogaster)
    Dmelanogaster$chr2L  # same as Dmelanogaster[["chr2L"]]

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

      ## 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(Dmelanogaster)) {
        cat("Checking sequence", seqname, "... ")
        seq <- Dmelanogaster[[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.Dmelanogaster.UCSC.dm3 version 1.3.11 Index]