README.md

In rforbiodatascience22/group_18_package: Simulates The Central Dogma of Biology

group_18_package

devtools::load_all(".")
#> ℹ Loading cdm
library(cdm)

Brief description of what the package is about :

This package contains a set of 5 functions , it allows the user to generate a DNA sequence of a given length using create_dna , that will be transcribed using the transcribe function , later the the get_codons function will allow the separation of the RNA seq into codons (3 bps ) , the vector of codons is used by join to be translate it into the appropriate amino acid and concatenated to from the primary structure of the peptide finally the last function (function five ) uses the result of the fourth above function and create a barplot to show the occurrance of each amino acid in the newly synthesized protein

How each function in the package works individually

Random DNA sequence

create_dna(size = 10)
#> [1] "GCGGTTACTC"

This creates a random DNA sequence, made of the four oligonucleotide, for the given length.

Transcribe

this function transcribes the DNA sequence into a mRNA one , converts the thymine T to Uracil U it takes a string and returs a string

transcribe("ATGC")
#> [1] "AUGC"

Getcodons

this function should take an RNA sequence (can be also a DNA ) in the form of a string as a first argument and an integer (start ) as a second argument that is meant to indicate from which base pair the reading frame should start . The function will return a vector of 3 letters string

get_codons(DNA_seq = "ATGCTG" , start = 1 )
#> [1] "ATG" "CTG"

Join

This function takes a vector of strings ( codons ) , converts each to it’s corresponding amino acid (as given by codon table ) and concatenate them , resulting in a peptide (returned as string)

AAseq("AUG")
#> [1] "M"

Function five

This function takes peptide sequence and returns a bar plot showing the occurance of each amino acid

aa_count

aa_count('AUGCGCUA')

How the functions in the package are used in conjuction with each other

Here we first generate a DNA sequence of 60 bps than we transcribe it(we only convert T -> U) to convert it to mRNA sequence from the resulting mRNA seq , the get_codons function create a vector of codons (3bps each) the translation occurs with the help of AA_seq function Finally the occurance of the different amino acids contained in the peptide is displayed in a bar plot

DNA<-create_dna(size = 60)
mRNA <-transcribe(DNA)
codons<-get_codons(mRNA)
peptide <- AAseq(codons)
aa_count(peptide)

rforbiodatascience22/group_18_package documentation built on April 5, 2022, 7:51 p.m.