Package: BSgenome.Ggallus.UCSC.galGal3
Title: Full genome sequences for Gallus gallus (UCSC version galGal3)
Description: Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects.
Version: 1.4.2
Suggests: GenomicFeatures
organism: Gallus gallus
common_name: Chicken
provider: UCSC
provider_version: galGal3
release_date: May 2006
release_name: WUSTL Gallus-gallus-2.1
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/galGal3/bigZips/
organism_biocview: Gallus_gallus
BSgenomeObjname: Ggallus
seqnames: paste("chr", c(1:28, 32, "M", "W", "Z", "E64", "E22C19W28_E50C23", paste(c(1:2, 4:8, 10:13, 16:18, 20, 22, 25, 28, "W", "Z", "E64", "E22C19W28_E50C23", "Un"), "_random", sep="")), sep="")
circ_seqs: "chrM"
SrcDataFiles: chromFa.tar.gz from http://hgdownload.cse.ucsc.edu/goldenPath/galGal3/bigZips/
PkgExamples: genome$chr1  # same as genome[["chr1"]]
	.
	## ---------------------------------------------------------------------
	## Upstream sequences
	## ---------------------------------------------------------------------
	## Starting with BioC 3.0, the upstream1000, upstream2000, and
	## upstream5000 sequences for galGal3 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("galGal3", "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.Ggallus.UCSC.galGal3/seqs