ngd 0.3.0

A comprehensive bioinformatics package with 21 essential programs

NGD - Bioinformatics Programs Package

A comprehensive Python package containing 21 essential bioinformatics programs for DNA/RNA analysis, sequence manipulation, and protein structure visualization.

Installation

You can install the package using pip:

pip install ngd

Or install from source:

git clone https://github.com/yourusername/ngd.git
cd ngd
pip install -e .

Available Programs

The package includes 21 comprehensive bioinformatics programs:

1. DNA Manipulation and Translation

• DNA sequence slicing and concatenation
• DNA to RNA transcription
• RNA to protein translation
• Basic sequence operations using Biopython

2. Reading FASTA Files

• Parse and read FASTA format files
• Extract sequence descriptions and data
• Handle multiple sequences in a single file

3. Writing and Reading GenBank Format

• Create GenBank records with annotations
• Write sequences to GenBank format
• Read and parse GenBank files
• Handle sequence metadata

4. Converting FASTA to GenBank with Annotations

• Convert between sequence formats
• Add annotations during conversion
• Batch processing of multiple sequences
• Format validation

5. Adding Features and Annotations to SeqRecord

• Create detailed sequence records
• Add gene features and annotations
• Modify sequence metadata
• Handle complex biological annotations

6. Fetching Sequences from NCBI using Entrez

• Access NCBI databases programmatically
• Retrieve GenBank records by ID
• Extract sequence information
• Handle NCBI API responses

7. Pairwise Sequence Alignment

• Align two DNA sequences
• Calculate alignment scores
• Visualize sequence similarities
• Handle alignment parameters

8. Multiple Sequence Alignment using MUSCLE

• Perform multiple sequence alignment
• Use external MUSCLE tool
• Handle alignment output
• Process alignment results

9. Constructing Phylogenetic Trees

• Build phylogenetic trees from alignments
• Calculate distance matrices
• Create UPGMA trees
• Visualize and save tree structures

10. PDB 3D Structure Visualization

• Download protein structures from PDB
• Parse mmCIF files
• Extract atomic coordinates
• Create 3D structure visualizations

11-21. Additional Bioinformatics Programs

• Placeholder programs ready for expansion
• Space for additional bioinformatics tools
• Extensible framework for new programs
• Ready for custom implementations

Usage

To view the code for any program, use the print_program function:

from ngd.programs import print_program

# Print program 1 (DNA Manipulation)
print_program(1)

# Print program 2 (FASTA Reading)
print_program(2)

# Print program 3 (GenBank Operations)
print_program(3)

# And so on for programs 4-21...

Requirements

The package requires the following dependencies:

• biopython >= 1.79 - Core bioinformatics functionality
• matplotlib >= 3.5.0 - Plotting and visualization
• numpy >= 1.21.0 - Numerical computations
• pandas >= 1.3.0 - Data manipulation
• requests >= 2.25.0 - HTTP requests for NCBI access

Features

• Comprehensive Coverage: From basic DNA manipulation to advanced phylogenetic analysis
• Educational: Well-commented code suitable for learning bioinformatics
• Practical: Real-world applications using popular bioinformatics tools
• Extensible: Easy to modify and extend for specific research needs
• Cross-platform: Works on Windows, macOS, and Linux
• Expandable: Framework supports up to 21 programs with room for growth

Examples

Basic DNA Operations

from ngd.programs import print_program
print_program(1)  # DNA manipulation and translation

Sequence Analysis

from ngd.programs import print_program
print_program(7)  # Pairwise sequence alignment

Database Access

from ngd.programs import print_program
print_program(6)  # NCBI sequence fetching

Placeholder Programs

from ngd.programs import print_program
print_program(11)  # Program 11 placeholder
print_program(21)  # Program 21 placeholder

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use this package in your research, please cite:

NGD Bioinformatics Package (2024). A comprehensive collection of bioinformatics programs.
Available at: https://pypi.org/project/ngd/