I would like to compare two DNAStrings that are larger than 20000 basepairs. I tried the matchPattern function from Biostrings package, however, I got this error:

Error in .valid.algos(pattern, max.mismatch, min.mismatch, with.indels,  :
  patterns with more than 20000 letters are not supported

There is a way to analyze these large strings in Bioconductor?

Hi Vinicius,

Maybe you want to try pairwiseAligment() for this. matchPattern() is probably not the right tool for comparing 2 strings. See ?pairwiseAligment for more information. The Biostrings package also has a nice vignette dedicated to Pairwise Sequence Alignments. See bioconductor.org/packages/Biostrings.

H.