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
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