Hi,

Is there a way to create a PDict object from amino acid sequences?

I would like to run a pattern search in a protein sequence for multiple pattern. With just one pattern I can do it with

       hits <- matchPattern("K", protein1)

but how can I do it, if I would like to search for e.g. c("K", "R")?

thanks

Assa

Hi Assa,

PDict objects are for DNA sequences only.  Please check matching of AAStringSet vs. another AAStringSet for a similar question and an efficient solution for the exact matching case based on CRAN package AhoCorasickTrie. If you need to perform inexact (a.k.a. fuzzy) matching, please check Creating a Biostrings PDict object from amino-acid sequences.

Cheers,

H.