Project for the course of Algorithms for Bioinformatics

Implementing Smith-Waterman algorithm in Python as a project for the course Algorithm for Bioinformatics, held by professor Enrico Blanzieri (A.Y 2022-2023).

Code

Libraries and modules

• NumPy
• itertools
• argparse

Cloning the repository

git clone https://github.com/iamandreatonina/Algorithms_bioinformatics.git

How to use the algorithm

python smith-waterman.py [-h] [-g GAP_PENALTY] [-m MATCH] [-p MISMATCH] [-o OUTPUT_NAME] seq1 seq2

By default without an output name, the code will also return a file text named SW_output

Options/parameters :

• First sequence [required], which corresponds to the rows of the matrix
• Second sequence [required], which are the columns of the matrix
• -h, --help [optional] which displays the helper and exit
• -g, -- gap_penalty [optional] scoring value for the gaps, by default is -1
• -m, -- match [optional] scoring value for the matches, by default is 2
• -p, -- mismatch [optional] scoring value for the mismatches, by default is -1
• -o, --output_name [optional] Name of the output file that will be created (default: SW_output)

Example

python3 smith-waterman.py ATCGGCGATA ATTATACGATA -g -2 -m 3 -p -1 -o alignment_output