Package: BSgenome.Dmelanogaster.UCSC.dm3
Title: Full genome sequences for Drosophila melanogaster (UCSC version dm3)
Description: Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects.
Version: 1.4.2
Suggests: TxDb.Dmelanogaster.UCSC.dm3.ensGene
organism: Drosophila melanogaster
common_name: Fly
provider: UCSC
provider_version: dm3
release_date: Apr. 2006
release_name: BDGP Release 5
source_url: http://hgdownload.cse.ucsc.edu/goldenPath/dm3/bigZips/
organism_biocview: Drosophila_melanogaster
BSgenomeObjname: Dmelanogaster
seqnames: paste("chr", c("2L", "2R", "3L", "3R", "4", "X", "U", "M", "2LHet", "2RHet", "3LHet", "3RHet", "XHet", "YHet", "Uextra"), sep="")
circ_seqs: "chrM"
SrcDataFiles: chromFa.tar.gz from http://hgdownload.cse.ucsc.edu/goldenPath/dm3/bigZips/
PkgExamples: genome$chr2L  # same as genome[["chr2L"]]
	.
	## ---------------------------------------------------------------------
	## Upstream sequences
	## ---------------------------------------------------------------------
	## Starting with BioC 3.0, the upstream1000, upstream2000, and
	## upstream5000 sequences for dm3 are not included in the BSgenome data
	## package anymore. However they can easily be extracted from the full
	## genome sequences with something like:
	.
	library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
	txdb <- TxDb.Dmelanogaster.UCSC.dm3.ensGene
	.
	## Because the chrU and chrUextra sequences are made of concatenated
	## scaffolds (see http://genome.ucsc.edu/cgi-bin/hgGateway?db=dm3),
	## extracting the upstream sequences for genes located on these
	## scaffolds is not reliable. So we exclude them:
	exclude <- c("chrU", "chrUextra")
	up1000seqs <- extractUpstreamSeqs(genome, txdb, width=1000,
	                                  exclude.seqlevels=exclude)
	.
	## 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 for more information.
seqs_srcdir: /fh/fast/morgan_m/BioC/BSgenomeForge/srcdata/BSgenome.Dmelanogaster.UCSC.dm3/seqs