Hi I am trying to work out how to relate basepair position information in unaligned sequence to aligned sequences in pairwiseAlignment objects. So if I have a feature in my initial unaligned pattern or subject sequence at 100-110 bp I would like to be able to identify where this in the aligned sequence taking into account any indels. Is there an easy way of getting this information or do I have to do some weird loop that scans through indels iteratively to calculate the new feature location?

Cheers

Hi,

Would the answer given here help you?

pairwiseAlignments coordinate mapping?

Cheers,

H.