PairwiseGenesComparison: Compare individual CDS from two genomes.

In lrjoshi/PairwiseGenesComparison: Compare individual genes (CDS) of two genomes

Description

This package can be used to compare indiviual genes of the two genomes. This package makes use of coding sequences format that can be found in Genbank. Right now, the package allows pairwise comparison of the genes of two genomes. You find detail manual in the github wiki section. You will need FASTA Nuceotide sequence files of the two genomes. These can be obtained from the Genbank. If you click on Send to button on Genbank, then you can select "Coding Sequences" and then FASTA Nucleotide or FASTA Protein sequences. Then you can run pairwise_genes_comparison() funtion in R. You have to provide path for two files and then you can run pairwise_genes_comaprison function on those two files. It will create a nice summary table output. It will also save the table as a csv file called "summary_table,csv" in the current folder. It uses DECIPHER package for pairwise alignment and to generate similarity matrix.

Usage

pairwise_genes_comparsion(filepath1, filepath2)

Arguments

filepath1= path to the first genome file

filepath2= path to the second genome file

Details

Dependency : DECIPHER, tidyverse,formattable, seqinr

Note

Make sure you have all the depedencies installed.

Author(s)

Lok Raj Joshi

Examples

#First create paths for the two files that you want to compare
filename1 <- paste("D:/Rpackages/gene1_sequence_format.txt")
filename2 <- paste("D:/Rpackages/gene2_sequence_format.txt")


#Then run pairwise_genes_comparison function using two filepaths
pairwise_genes_comparsion(filename1, filename2)

lrjoshi/PairwiseGenesComparison documentation built on Aug. 5, 2020, 2:20 a.m.