jayoung

I now see that there's another class that I could have use for my alignments: ?DNAMultipleAlignment but I don't think it helps me with codons/translation.

hi @sdalin, I don't know if Herve had time to add anything to Biostrings, but in the meantime here is an ad hoc solution I used. I only accounted for...

I can see the challenge! It could get to be more like an alignment problem, where you might want to have different scores/penalties for mismatches versus extending length. In fact,...

after a bit more testing, I'm not sure it's true that findPalindromes() will always find and report the palindrome with longest arms: ``` palindromeLeftArm(findPalindromes(BString("abcXefghijNOPQRSTjihgfedcba"), max.mismatch=1, max.looplength=8), max.mismatch=1) # Views on...

yes, in my (likely unusual) use case, the palindromes should be centered at the read center, so I think pairwiseAlignment on the halves should work. The molecular biology should have...

Thanks, all - this looks great. One idea to handle the multiple short matches is to add an option to choose the palindrome with longest arms, or just let the...

oh, I get it now! Thanks. I hadn't understood that from ?findPalindromes Would it make sense to disallow running palindromeLeftArm/palindromeRightArm/palindromeArmLength functions directly on XString objects, like I tried to do?...

Thanks for clarifying the man page - that'll help. In your use case where you run findPalindromes() on a full genome and then later run palindromeLeftArm() etc on the fasta...

hi there, try using the ranges() function on your findPalindromes result, perhaps as.data.frame(ranges()). Does that work? Janet > On May 6, 2021, at 1:20 AM, meyerlaker ***@***.***> wrote: > >...

yes, support is a better place for it. I was a bit confused that I didn't see it here, just in my email. I like your new as.data.frames!