Count amino acid in protein sequence in R

Question

[boaty]

Hello,

Is there any tools to count occurrence of amino acid in protein sequence like this:

string_count("AAA","AA")#count "AA" in sequence "AAA"
[1] 2 #result, so 2 "AA"

I used stringr package but it gives us this:

library(stringr)
str_count("AAA","AA")
[1] 1 #result, only 1 "AA"

But now I want to give a reasonably higher score for longer peptide. So is there any tools for this?

Thanks a lot

[Bastien Hervé]

It is not very clear what is your problem and what you want to achieve.

Is the result of str_count correct to you ? Or do you want str_count("AAA","AA") to result as 2 counts

What kind of score do you want to apply ? Could you share an example ?

[boaty]

thanks Bastien, sorry my question was unclear. I want str_count("AAA","AA") to result as 2 counts. for instance, "AAAAAA" will give 5 counts and "AARAAGAAN" gives us 3 counts. This counting strategy will give continuous peptide (like "AAAAAA") more counts.

[Bastien Hervé]

See ATpoint 's answer for the count part. And for the score, if you want to play it dirty you can divide the number of count by the peptide length or create your own score strategy using the start and end position in the result of matchPattern. Like increase the score till df[end] < df[start+1]+1, or something similar

[boaty]

this is an advice from a real expert! YES, a scoring strategy, this is what i want to do after all exploratory analysis

[WouterDeCoster]

Hi boaty,

If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted.

Thanks!

[boaty]

sorry for it. it's done now

Answer 1

[ATpoint]

Use the Biostring package from BioC:

matchPattern("AA", AAString("AAA"))

will produce:

Views on a 3-letter AAString subject
subject: AAA
views:
    start end width
[1]     1   2     2 [AA]
[2]     2   3     2 [AA]

[boaty]

thanks ATpoint, by using your suggestion, I got very good result. Thank you. here's my code for my counting :

peptide_count <- lapply(peptides, function(x) {#peptides, a list of peptides
  peptide=x
  length(unique(c(ranges(matchPattern(peptide, AAString(prot_seq))), #prot_seq : protein sequence to search on
                   ranges(matchPattern(reverse(peptide), AAString(prot_seq))))
            )
    )
})

some additional functions are added to make +/- peptide (like "RY" and "YR") as the same thing. because in this study, reverse peptide is no different to original peptide. In stringr, str_count("RY|YR","RYYRRYRY") can do it. But matchPattern somehow can't, so sorry, I make my code complex .....