Use matchPattern for large DNAStrings
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@vinicius-henrique-da-silva-6713
Last seen 2.1 years ago
Brazil

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?

biostrings annotate • 637 views
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@herve-pages-1542
Last seen 18 hours ago
Seattle, WA, United States

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.

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