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Question: creating PDIct from AAStringSets
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gravatar for Assa Yeroslaviz
7 months ago by
Assa Yeroslaviz1.3k
Munich, Germany
Assa Yeroslaviz1.3k wrote:

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

ADD COMMENTlink modified 7 months ago by Hervé Pagès ♦♦ 12k • written 7 months ago by Assa Yeroslaviz1.3k
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gravatar for Hervé Pagès
7 months ago by
Hervé Pagès ♦♦ 12k
United States
Hervé Pagès ♦♦ 12k 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.

Cheers,

H.

ADD COMMENTlink written 7 months ago by Hervé Pagès ♦♦ 12k
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