Question: creating PDIct from AAStringSets
gravatar for Assa Yeroslaviz
22 months ago by
Assa Yeroslaviz1.4k
Munich, Germany
Assa Yeroslaviz1.4k wrote:


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")?




ADD COMMENTlink modified 22 months ago by Hervé Pagès ♦♦ 13k • written 22 months ago by Assa Yeroslaviz1.4k
gravatar for Hervé Pagès
22 months ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

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.



ADD COMMENTlink written 22 months ago by Hervé Pagès ♦♦ 13k
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