smoothMiner (version 0.1-10)

upstream: CSHinteg06 data resources -- yeast upstream sequence data

Usage

data(sceUpstream)

format

See the examples.

source

The source is SGD website, Download Data->FTP->sequence->genomic_sequence->orf_dna->archive utr5_sc_500.20040206.fasta.gz

ftp://ftp.yeastgenome.org/yeast/sequence/genomic_sequence/orf_dna/archive/utr3_sc_500.20040206.fasta.gz

References

See the upstream.Rnw vignette for details.

Examples

data(sceUpstream)
sceUpstream
keys(sceUpstream)[1:3]
u1 = getUpstream("YAL001C", sceUpstream)
Nmers( u1[[1]], 6, TRUE)[1:5]
# now look at hexamers
#if (!exists("sceU500hex")) data(sceU500hex)
#names(sceU500hex)[1:4]
#sceU500hex[[1]][1:5]
if (!exists("hexFrqMat")) data(hexFrqMat)
hexFrqMat
# look at occurrences of AAAAAA
aac = which.max(hexFrqMat[1,])
aac
hexFrqMat[1,(aac-3):(aac+3),drop=FALSE]
# which hexamer is most common for a certain gene
gm = which.max(hexFrqMat[,"YHR126C"])
gm
wg = which(colnames(hexFrqMat)=="YHR126C")
wg
hexFrqMat[gm,(wg-3):(wg+3),drop=FALSE]

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