[BioC] matching sRNA sequences with whole data
vobencha at fhcrc.org
Tue Aug 9 17:37:49 CEST 2011
The "Biostrings BSgenome Overview" link on this page is a great summary
of string matching,
Specifically, I think the vmatchPattern() and matchPDict() functions
will be most helpful to you.
On 08/08/2011 04:25 AM, chawla wrote:
> 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.
> I tried
> 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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