Full genome sequences for Caenorhabditis elegans (UCSC version ce2)

Description

Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) 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/ce2/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.Celegans.UCSC.ce2
genome <- BSgenome.Celegans.UCSC.ce2
seqlengths(genome)
genome$chrI  # same as genome[["chrI"]]

## ---------------------------------------------------------------------	## Upstream sequences
## ---------------------------------------------------------------------
## Starting with BioC 3.0, the upstream1000, upstream2000, and
## upstream5000 sequences for ce2 are not included in the BSgenome data
## package anymore. However they can easily be extracted from the full
## genome sequences with something like:

library(GenomicFeatures)
txdb <- makeTranscriptDbFromUCSC("ce2", "refGene")
gn <- sort(genes(txdb))
up1000 <- flank(gn, width=1000)
up1000seqs <- getSeq(genome, up1000)

## IMPORTANT: Make sure you use a TxDb package (or TranscriptDb object),
## that contains a gene model based on the exact same reference genome
## as the BSgenome object you pass to getSeq(). Note that you can make
## your own custom TranscriptDb object from various annotation resources.
## See the makeTranscriptDbFromUCSC(), makeTranscriptDbFromBiomart(),
## and makeTranscriptDbFromGFF() functions in the GenomicFeatures
## package.

## ---------------------------------------------------------------------
## 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

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> library(BSgenome.Celegans.UCSC.ce2)
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.Celegans.UCSC.ce2/package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: BSgenome.Celegans.UCSC.ce2
> ### Title: Full genome sequences for Caenorhabditis elegans (UCSC version
> ###   ce2)
> ### Aliases: BSgenome.Celegans.UCSC.ce2-package BSgenome.Celegans.UCSC.ce2
> ###   Celegans
> ### Keywords: package data
> 
> ### ** Examples
> 
> BSgenome.Celegans.UCSC.ce2
Worm genome:
# organism: Caenorhabditis elegans (Worm)
# provider: UCSC
# provider version: ce2
# release date: Mar. 2004
# release name: WormBase v. WS120
# 7 sequences:
#   chrI   chrII  chrIII chrIV  chrV   chrX   chrM                              
# (use 'seqnames()' to see all the sequence names, use the '$' or '[[' operator
# to access a given sequence)
> genome <- BSgenome.Celegans.UCSC.ce2
> seqlengths(genome)
    chrI    chrII   chrIII    chrIV     chrV     chrX     chrM 
15080483 15279308 13783313 17493791 20922231 17718849    13794 
> genome$chrI  # same as genome[["chrI"]]
  15080483-letter "DNAString" instance
seq: GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA...TTAGGCTTAGGCTTAGGCTTAGGTTTAGGCTTAGGC
> 
> ## ---------------------------------------------------------------------	## Upstream sequences
> ## ---------------------------------------------------------------------
> ## Starting with BioC 3.0, the upstream1000, upstream2000, and
> ## upstream5000 sequences for ce2 are not included in the BSgenome data
> ## package anymore. However they can easily be extracted from the full
> ## genome sequences with something like:
> 
> library(GenomicFeatures)
Loading required package: AnnotationDbi
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> txdb <- makeTranscriptDbFromUCSC("ce2", "refGene")
Error: could not find function "makeTranscriptDbFromUCSC"
Execution halted