[BioC] matching sRNA sequences with whole data
chawla at bio.ntnu.no
Mon Aug 8 13:25:59 CEST 2011
I want to know the faster method of obtaining the frequency of only
perfect matches between a data seq and seq target file
both are set of nucleotide sequences but in large numbers.
for (i in 1:100)
#for (i in 1:nrow(urfreq))
Since the target datafile is huge , this piece of code take 22 min for
only 100 sequences , while I need to find frequency of over 3 million
sequences in the three samples data(glr 4 5 and 6).
Is there any package/function for such matching.
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