Calculating edit distance of two sequences using 4 Russians method

Build project

make

This will generate two files

main
generator

Run project

generator

By running generator you will get output file containing two random sequences, each string in a single line. When running generator you can specify the length of the generated strings (default value 100). generator usage:

./generator [inputFilename, firstSequenceLength, secondSequenceLength]

default filename is input.txt, default sequence length is 100. If only a single (first) sequence length is provided, both sequences will have the same length.

Example runs:

./generator
./generator twoSequences.txt
./generator input 1000 12000

First example will generate a file input.txt with two sequences of length 1000, each in its own line. Second example will generate same thing, but in file twoSequences.txt Third example will generate two sequences of length 1000 and 12000, and store it to file 'input'

main

After generating the strings, you can run the main file to get the edit distance between those two sequences. main takes 3 arguments; block size, input file name (containing two sequences) and output file name (in MAF format).

./main block_size input_file.txt output.maf

help message is generated on run with insufficient or incorrect parameters.

Authors

• Authors: Marko Čepo, Tomislav Lokotar
• Project made as part of Bionformatics course at Faculty of Electrical Engineering and Computing, fall 2017/2018
• Link to course: https://www.fer.unizg.hr/predmet/bio