Package: BSgenome.Btaurus.UCSC.bosTau3
Title: Full genome sequences for Bos taurus (UCSC version bosTau3)
Description: Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects.
Version: 1.4.2
Suggests: GenomicFeatures
organism: Bos taurus
common_name: Cow
provider: UCSC
provider_version: bosTau3
release_date: Aug. 2006
release_name: Baylor College of Medicine HGSC Btau_3.1
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/bosTau3/bigZips/
organism_biocview: Bos_taurus
BSgenomeObjname: Btaurus
SrcDataFiles: bosTau3.2bit from http://hgdownload.soe.ucsc.edu/goldenPath/bosTau3/bigZips/
PkgExamples: genome$chr1  # same as genome[["chr1"]]
	.
	## ---------------------------------------------------------------------
	## Upstream sequences
	## ---------------------------------------------------------------------
	## UCSC makes the upstream sequences for bosTau3 available for download
	## here http://hgdownload.soe.ucsc.edu/goldenPath/bosTau3/bigZips/
	## Alternatively, the upstream sequences can be extracted from the full
	## genome sequences with something like:
	.
	library(GenomicFeatures)
	txdb <- makeTxDbFromUCSC("bosTau3", "refGene")
	up1000seqs <- extractUpstreamSeqs(genome, txdb, width=1000)
	.
	## See ?extractUpstreamSeqs in the GenomicFeatures package for more
	## information about this.
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Btaurus.UCSC.bosTau3/seqs
seqfile_name: bosTau3.2bit