That's perfect. Thanks for the quick response. Andrew
On Wed, Apr 28, 2010 at 8:16 PM, Patrick Aboyoun <[email protected]> wrote: > Andrew, > > start(subject(myalign)) > > should get you what you are looking for. > > Cheers, > Patrick > > > > On 4/28/10 5:07 PM, Andrew Yee wrote: > >> I'm using pairwiseAlignment() in the Biostrings package as follows: >> >> >> library('Biostrings') >> >> pattern<- DNAString('GCGAGAG') >> subject<- DNAString('AGCTTTAGAGGCGAGAGGCAT') >> >> myalign<- pairwiseAlignment(pattern, subject) >> subject(myalign) >> >> >> >>> subject(myalign) >>> >>> >> [11] GCGAGAG >> >> I'm interested in the position where the pattern starts aligning with the >> subject. In this case, subject(myalign) gives 11 as the starting position >> as part of the print out. Is there a way to pull out this starting >> position >> information from subject(myalign)? >> >> Thanks, >> Andrew >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioc-sig-sequencing mailing list >> [email protected] >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing >> >> > > [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
