CODEWITHSUNDEEP
rcountbioinformaticsfasta
Rea Kalampaliki
Rea Kalampaliki

Reputation: 164

How to count amino acids in a FASTA file with multiple protein sequences, using R

Having a fasta file containing protein sequences like these two showing below, I would like to count how many times the amino acid A appears in each sequence. 

>sp|P01920|DQB1_HUMAN HLA class II histocompatibility antigen, DQ beta 1 chain OS=Homo sapiens OX=9606 GN=HLA-DQB1 PE=1 SV=2
MSWKKALRIPGGLRAATVTLMLAMLSTPVAEGRDSPEDFVYQFKAMCYFTNGTERVRYVT
RYIYNREEYARFDSDVEVYRAVTPLGPPDAEYWNSQKEVLERTRAELDTVCRHNYQLELR
TTLQRRVEPTVTISPSRTEALNHHNLLVCSVTDFYPAQIKVRWFRNDQEETTGVVSTPLI
RNGDWTFQILVMLEMTPQHGDVYTCHVEHPSLQNPITVEWRAQSESAQSKMLSGIGGFVL
GLIFLGLGLIIHHRSQKGLLH

>sp|P18440|ARY1_HUMAN Arylamine N-acetyltransferase 1 OS=Homo sapiens OX=9606 GN=NAT1 PE=1 SV=2
MDIEAYLERIGYKKSRNKLDLETLTDILQHQIRAVPFENLNIHCGDAMDLGLEAIFDQVV
RRNRGGWCLQVNHLLYWALTTIGFETTMLGGYVYSTPAKKYSTGMIHLLLQVTIDGRNYI
VDAGFGRSYQMWQPLELISGKDQPQVPCVFRLTEENGFWYLDQIRREQYIPNEEFLHSDL
LEDSKYRKIYSFTLKPRTIEDFESMNTYLQTSPSSVFTSKSFCSLQTPDGVHCLVGFTLT
HRRFNYKDNTDLIEFKTLSEEEIEKVLKNIFNISLQRKLVPKHGDRFFTI

This code

library(seqinr)
data <- read.fasta(file = "yourlist.fasta", as.string = TRUE)
library(stringr)
ACount <- stri_count_regex("A",data)

gives the result showing on the picture.enter image description here

Although the character A excists in both sequences they are not counted. Any ideas on why is this happening? Thank you for your interest.

Upvotes: 0

Views: 1398

Answers (2)

dqt
dqt

Reputation: 41

There seem to be some mistakes on your code. Following your procedure, this worked fine by me:

library(seqinr)
data <- read.fasta(file = "yourlist.fasta", seqtype = "AA", as.string = TRUE, set.attributes = FALSE)

library(stringi)
ACount <- stri_count_regex(data, "A")

You have to specify with the seqtype argument the type of sequence, being "DNA" the default. You have to change it to "AA" (protein). The stri_count_regex function is part of the stringi base R package.

I get now:

> str(ACount)
 int [1:2] 14 7

Upvotes: 0

Mel_M
Mel_M

Reputation: 3

I have some idea how I would do this, but I'm not sure if it will work in your string, but I thought I'd answer. You can probably detect a string using the package stringr, using str_count. Here's some info https://stringr.tidyverse.org/reference/str_detect.html

I just made a short example with your string above. 

dna<- "MDIEAYLERIGYKKSRNKLDLETLTDILQHQIRAVPFENLNIHCGDAMDLGLEAIFDQVVRRNRGGWCLQVNHLLYWALTTIGFETTMLGGYVYSTPAKKYSTGMIHLLLQVTIDGRNYIVDAGFGRSYQMWQPLELISGKDQPQVPCVFRLTEENGFWYLDQIRREQYIPNEEFLHSDLLEDSKYRKIYSFTLKPRTIEDFESMNTYLQTSPSSVFTSKSFCSLQTPDGVHCLVGFTLTHRRFNYKDNTDLIEFKTLSEEEIEKVLKNIFNISLQRKLVPKHGDRFFTI"

str_count(string= dna, pattern= "VGFTL")
#1

Or I saw online the package sequences but it only counts the ’A’, ’C’, ’G’ and ’T’ bases, so that's not going to show you a string. Here is the cran just in case you want to take a look. https://cran.r-project.org/web/packages/sequences/sequences.pdf

Upvotes: 0

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