https://github.com/bibymaths/sequencealigner
A simple C++ program for performing Longest Common Subsequence (LCS), Global Alignment, and Local Alignment using dynamic programming. Reads sequences from input files and computes alignment scores based on match, mismatch, and gap penalties.
https://github.com/bibymaths/sequencealigner
Last synced: about 1 year ago
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A simple C++ program for performing Longest Common Subsequence (LCS), Global Alignment, and Local Alignment using dynamic programming. Reads sequences from input files and computes alignment scores based on match, mismatch, and gap penalties.
- Host: GitHub
- URL: https://github.com/bibymaths/sequencealigner
- Owner: bibymaths
- License: mit
- Created: 2025-03-20T12:40:50.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-03-20T13:29:36.000Z (about 1 year ago)
- Last Synced: 2025-03-20T14:04:33.156Z (about 1 year ago)
- Language: C++
- Size: 9.77 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Sequence Alignment Program
## Description
This C++ program performs sequence alignment using three different methods:
1. **Longest Common Subsequence (LCS)**: Finds the length of the longest common subsequence between two sequences.
2. **Global Alignment**: Uses a scoring system with match, mismatch, and gap penalties to align two sequences globally.
3. **Local Alignment**: Identifies the best local alignment between two sequences based on a scoring system.
## Requirements
- C++ compiler (e.g., `g++`)
- Input sequence files (`seq1.txt` and `seq2.txt`)
## Compilation
To compile the program, run:
```sh
g++ -o sequence_alignment sequence_alignment.cpp
```
## Usage
Run the program from the terminal:
```sh
./sequence_alignment
```
Then, enter your choice of alignment method:
- `1` for LCS
- `2` for Global Alignment
- `3` for Local Alignment
## Input Format
The program reads two DNA or protein sequences from text files:
- `seq1.txt` (First sequence)
- `seq2.txt` (Second sequence)
Each file should contain a single line with the sequence.
## Output
- LCS method prints the length of the longest common subsequence.
- Global and Local alignment methods print the alignment score.
## Example
**Input files:**
```
seq1.txt:
ATGCTGA
seq2.txt:
ATGTTGA
```
**Running the program:**
```sh
./sequence_alignment
Select Alignment Method:
1. LCS
2. Global
3. Local
Choice: 2
```
**Output:**
```
Global Alignment Score: 10
```
## License
This program is open-source and free to use for educational purposes.