RPTRF

RPTRF: A Rapid Perfect Tandem Repeat Finder Tool for DNA Sequences
The article is available on ScinceDirect: https://authors.elsevier.com/c/1gjMo14z5I5bo0

In this manual, you can find guidelines for running the executable file and compiling the RPTRF from the source code.

Table of contents

• Run the executable
• Compile the source code

Run the executable

To run the executable file, you may follow the bellow steps:

1. Download the repository and unzip the file.
2. Get access to the executable file from executable/RPTRF path or the Releases section of the repository.

cd executable/

3. Make the RPTRF executable by the following command:

sudo chmod +x RPTRF

4. Input sequence can be obtained from dataset/Sample.fasta directory, downloaded from the NCBI website (GRCh38), or you may use your local DNA sequence in .Fasta format.
5. To run the RPTRF with the default settings and the sample sequence, enter the following command(the output file will be created in your current directory):

./RPTRF -s ../dataset/sample.fasta

6. To use optional arguments use the following command(argument explanation is provided in the following table):

./RPTRF -s ../dataset/sample.fasta -m 100 -t 10

Arguments table:

Flag	Definition	Default
-s	Input .Fasta sequnce path
-m	Maximum motif size	100
-t	Minimum length of tandem repeats	10
-h	Access to manual in the command line

Output File Format:
Tandem repeats of the given sequence will be reported as result-X.txt in your current directory. The result-X.txt file has four columns each indicating the following information:

Start	End	Len	Motif length( Sequence )
The starting point of the Tandem Repeat	Ending point of the Tandem Repeat	The length of the Tandem Repeat	Motif Size(the motif that is repeated in the Tandem Repeat)

Compile the source code

The source code can be compiled with the following instructions:

1. Download the repository and unzip the file
2. Get the source code of RPTRF from src/ directory
3. Ensure that you have installed boost-devel package. To install the package use the following command:

sudo apt-get install libboost-all-dev

4. Once the package is installed, run the following command to compile the source code:

g++ -fopenmp RPTRF.cpp -O3 -o RPTRF

5. The binary file will be named as: ./RPTRF.

6. To use the RPTRF follow the step 4 or 5 of Executing section.