Hi all,

I'm new to this mailing list and have a very simple question about digestion
with restriction enzyme for the whole genome.

I'm using package BSgenome.Hsapiens.UCSC.hg18 to find the cut site of
enzyme. Is there a faster way (ie. pre-built package) to get the fragment
sequence and it's location in UCSC genome browser format (Chr#: start bp -
end bp).

I'm planning on finding the restriction site location, then find the
substring between two consecutive cut sites.

Is there any faster way to do this?

Here's the code that I'm thinking of:

library(BSgenome.Hsapiens.UCSC.hg18)
c1<-Hsapiens$chr1
m<-matchPatterns('CTAG', c1)

#And the for loop
reslt<-NULL
for (i in 1:(length(m)-1)) {
   reslt<-rbind(reslt, cbind(start(m[i])+1, start(m[i+1])-3,
getSeq(Hsapiens, 'chr1', start(m[i])+2, start(m[i+1])-2)))
}

It seems like this code is no where near perfect. Please give me some input.

Thanks

-- 
Regards,
Anh Tran

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