Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer2)

Description

Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer2, June 2008) and stored in Biostrings objects.

Note

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

chromFa.tar.gz from http://hgdownload.cse.ucsc.edu/goldenPath/sacCer2/bigZips/
  

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

Author(s)

The Bioconductor Dev Team

See Also

• BSgenome objects and the available.genomes function in the BSgenome software package.

• DNAString objects in the Biostrings package.

• The BSgenomeForge vignette (vignette("BSgenomeForge")) in the BSgenome software package for how to make a BSgenome data package.

Examples

BSgenome.Scerevisiae.UCSC.sacCer2
genome <- BSgenome.Scerevisiae.UCSC.sacCer2
seqlengths(genome)
genome$chrI  # same as genome[["chrI"]]

## ---------------------------------------------------------------------
## Genome-wide motif searching
## ---------------------------------------------------------------------
## 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")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BSgenome.Scerevisiae.UCSC.sacCer2)
Loading required package: BSgenome
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/BSgenome.Scerevisiae.UCSC.sacCer2/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BSgenome.Scerevisiae.UCSC.sacCer2
> ### Title: Saccharomyces cerevisiae (Yeast) full genome (UCSC version
> ###   sacCer2)
> ### Aliases: BSgenome.Scerevisiae.UCSC.sacCer2-package
> ###   BSgenome.Scerevisiae.UCSC.sacCer2 Scerevisiae
> ### Keywords: package data
> 
> ### ** Examples
> 
> BSgenome.Scerevisiae.UCSC.sacCer2
Yeast genome:
# organism: Saccharomyces cerevisiae (Yeast)
# provider: UCSC
# provider version: sacCer2
# release date: June 2008
# release name: SGD June 2008 sequence
# 18 sequences:
#   chrI    chrII   chrIII  chrIV   chrV    chrVI   chrVII  chrVIII chrIX  
#   chrX    chrXI   chrXII  chrXIII chrXIV  chrXV   chrXVI  chrM    2micron
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)
> genome <- BSgenome.Scerevisiae.UCSC.sacCer2
> seqlengths(genome)
   chrI   chrII  chrIII   chrIV    chrV   chrVI  chrVII chrVIII   chrIX    chrX 
 230208  813178  316617 1531919  576869  270148 1090947  562643  439885  745742 
  chrXI  chrXII chrXIII  chrXIV   chrXV  chrXVI    chrM 2micron 
 666454 1078175  924429  784333 1091289  948062   85779    6318 
> genome$chrI  # same as genome[["chrI"]]
  230208-letter "DNAString" instance
seq: CCACACCACACCCACACACCCACACACCACACCACA...GGTGTGTGGGTGTGGTGTGGGTGTGGTGTGTGTGGG
> 
> ## ---------------------------------------------------------------------
> ## Genome-wide motif searching
> ## ---------------------------------------------------------------------
> ## 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")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
> 
Unescaped left brace in regex is deprecated, passed through in regex; marked by <-- HERE in m/%{ <-- HERE (.*?)}/ at /usr/bin/run-mailcap line 528.