Package: BSgenome.Celegans.UCSC.ce2
Title: 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.
Version: 1.4.2
Suggests: GenomicFeatures
organism: Caenorhabditis elegans
common_name: Worm
provider: UCSC
provider_version: ce2
release_date: Mar. 2004
release_name: WormBase v. WS120
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/ce2/bigZips/
organism_biocview: Caenorhabditis_elegans
BSgenomeObjname: Celegans
seqnames: paste("chr", c("I", "II", "III", "IV", "V", "X", "M"), sep="")
circ_seqs: "chrM"
SrcDataFiles: chromFa.zip from http://hgdownload.cse.ucsc.edu/goldenPath/ce2/bigZips/
PkgExamples: 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 <- makeTxDbFromUCSC("ce2", "refGene")
	gn <- sort(genes(txdb))
	up1000 <- flank(gn, width=1000)
	up1000seqs <- getSeq(genome, up1000)
	.
	## IMPORTANT: Make sure you use a TxDb package (or TxDb 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 TxDb object from various annotation resources.
	## See the makeTxDbFromUCSC(), makeTxDbFromBiomart(),
	## and makeTxDbFromGFF() functions in the GenomicFeatures
	## package.
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Celegans.UCSC.ce2/seqs