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https://github.com/bibymaths/perl_snippets
A collection of Perl scripts for solving bioinformatics problems and algorithmic challenges, including sequence analysis, alignment, and DNA assembly.
https://github.com/bibymaths/perl_snippets
alignment amino-acids assembly bioinofrmatics dna-sequences edit-distance fibonacci hamming-distance lcs motif perl
Last synced: 8 days ago
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A collection of Perl scripts for solving bioinformatics problems and algorithmic challenges, including sequence analysis, alignment, and DNA assembly.
- Host: GitHub
- URL: https://github.com/bibymaths/perl_snippets
- Owner: bibymaths
- License: mit
- Created: 2025-01-18T21:19:05.000Z (9 days ago)
- Default Branch: main
- Last Pushed: 2025-01-18T21:22:49.000Z (9 days ago)
- Last Synced: 2025-01-18T22:24:08.093Z (9 days ago)
- Topics: alignment, amino-acids, assembly, bioinofrmatics, dna-sequences, edit-distance, fibonacci, hamming-distance, lcs, motif, perl
- Language: Perl
- Homepage:
- Size: 9.77 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Bioinformatics and Algorithmic Problem Solvers
This repository contains a collection of scripts designed to solve common problems in bioinformatics and algorithmic puzzles. These Perl scripts can be utilized for DNA sequence analysis, optimization problems, and mathematical challenges.
## Table of Contents
1. [Scripts Overview](#scripts-overview)
2. [Requirements](#requirements)
3. [Usage](#usage)
4. [Scripts Description](#scripts-description)
5. [License](#license)
---
## Scripts Overview
| Script Name | Description |
|----------------------------------|----------------------------------------------|
| `fibonacci_series_calculator.pl` | Generates Fibonacci series numbers. |
| `tower_of_hanoi_solver.pl` | Solves the Tower of Hanoi puzzle. |
| `dna_distinct_substrings.pl` | Finds all distinct substrings in DNA data. |
| `hamming_distance_calculator.pl` | Calculates the Hamming distance between sequences. |
| `amino_acid_to_dna_converter.pl` | Converts amino acid sequences to DNA codons. |
| `global_alignment_wunsch.pl` | Performs global sequence alignment using the Needleman-Wunsch algorithm. |
| `local_alignment_smith.pl` | Performs local sequence alignment using the Smith-Waterman algorithm. |
| `edit_distance_calculator.pl` | Computes edit distance between strings. |
| `motif_identification_profile.pl`| Identifies motifs using profile matrices. |
| `longest_common_subsequence.pl` | Finds the longest common subsequence between strings. |
| `dna_fragment_assembly.pl` | Assembles DNA fragments into sequences. |
---
## Requirements
- **Perl**: Ensure you have Perl installed on your system. Most Unix-based systems come with Perl pre-installed.
## Usage
1. Clone this repository:
```bash
git clone https://github.com/your-username/bioinformatics-scripts.git
cd bioinformatics-scripts
```
2. Run the scripts using Perl:
```bash
perl script_name.pl
```
3. For scripts requiring input, provide the necessary arguments or input files as specified in the script comments.
---
## Scripts Description
### `fibonacci_series_calculator.pl`
Generates Fibonacci numbers up to a specified limit. Useful for sequence-based problems.
### `tower_of_hanoi_solver.pl`
Solves the Tower of Hanoi puzzle and outputs the steps required to move all disks from one peg to another.
### `dna_distinct_substrings.pl`
Analyzes a given DNA sequence and outputs all distinct substrings, aiding in sequence pattern recognition.
### `hamming_distance_calculator.pl`
Calculates the Hamming distance between two DNA or RNA sequences, measuring the number of differing nucleotides.
### `amino_acid_to_dna_converter.pl`
Converts amino acid sequences back into possible DNA codons, useful for reverse translation.
### `global_alignment_wunsch.pl`
Implements the Needleman-Wunsch algorithm for aligning two sequences globally.
### `local_alignment_smith.pl`
Implements the Smith-Waterman algorithm for local alignment of sequences.
### `edit_distance_calculator.pl`
Computes the minimum number of edits required to transform one string into another.
### `motif_identification_profile.pl`
Uses profile matrices to identify motifs in DNA sequences.
### `longest_common_subsequence.pl`
Finds the longest subsequence common to two given sequences.
### `dna_fragment_assembly.pl`
Reconstructs DNA sequences from smaller fragments using sequence overlaps.
---
## License
This repository is licensed under the MIT License. See the `LICENSE` file for details.