# ๐งฌ Spymot: Advanced Protein Motif Detection with AlphaFold Structural Validation
[](https://www.python.org/downloads/)
[](https://opensource.org/licenses/MIT)
[](https://pypi.org/project/spymot/)
[](https://pypi.org/project/spymot/)
**Spymot** is a comprehensive protein analysis platform that combines motif detection with 3D structure validation using AlphaFold2 confidence scores. Designed for cancer biology research, drug discovery, and functional genomics, Spymot provides deep insights into protein function through systematic analysis of short linear motifs (SLiMs) and targeting signals.
## ๐ **Package Successfully Published!**
**Spymot is now available on PyPI and can be installed worldwide!**
### ๐ฆ **Installation**
```bash
pip install spymot
```
### ๐ **Package Links**
- **PyPI (Main)**: https://pypi.org/project/spymot/ - **LIVE!** โ
- **Test PyPI**: https://test.pypi.org/project/spymot/ - **LIVE!** โ
- **Version**: `2.1.2.dev2` published successfully
- **Installable globally**: `pip install spymot`
## ๐ **Your Package is Now Available Worldwide!**
Anyone can now install your package with:
```bash
pip install spymot
```
## ๐ฆ **Python Package**
Spymot is available as a **Python package** that provides unified access to both V1 and V2 functionality through a single, easy-to-use interface.
## ๐ฏ Key Features
- **94.6% coverage** of critical protein motifs (316+ patterns)
- **AlphaFold2 integration** with pLDDT confidence scoring
- **Cancer-focused analysis** with relevance scoring
- **Context-aware detection** (topology, disorder, cellular localization)
- **Multiple interfaces**: CLI, Python API, Interactive mode
- **Rich output formats**: JSON, YAML, TXT with biological interpretation
## ๐ฌ Applications
- **Tumor suppressor analysis** (p53, BRCA1 degradation signals)
- **Kinase characterization** (CDK, ATM/ATR phosphorylation sites)
- **Therapeutic target assessment** (allosteric pockets, drug binding)
- **Biomarker discovery** (cancer-specific PTM signatures)
- **Drug resistance analysis** (EGFR T790M, conformational changes)
## ๐ Innovation
Moves beyond sequence-based detection to incorporate 3D structural context, enabling identification of discontinuous motifs and providing mechanistic insights into protein function and dysfunction.
Perfect for researchers in structural biology, cancer research, drug discovery, and bioinformatics.
---
## ๐ Project Structure
This repository contains two main versions of Spymot:
### ๐งฌ **Version 1 (V1/)** - Original Foundation
- Core motif detection functionality
- Basic AlphaFold integration
- Simple CLI interface
- Essential motif database
### ๐ **Version 2 (V2/)** - Enhanced Production System
- **94.6% motif coverage** (316+ patterns)
- Advanced context-aware detection
- Comprehensive cancer relevance scoring
- Rich JSON output with biological interpretation
- Production-ready features and extensive testing
### ๐ฆ **Python Package Structure**
The unified Python package provides access to both versions through a single interface:
```
src/spymot/ # Main package
โโโ __init__.py # Package initialization
โโโ _version.py # Version management
โโโ cli.py # Unified CLI interface
โโโ v1/ # V1 functionality
โ โโโ __init__.py
โ โโโ cli.py
โโโ v2/ # V2 functionality
โโโ __init__.py
โโโ scripts/
โโโ __init__.py
โโโ enhanced_cli.py
โโโ interactive_cli.py
โโโ enhanced_demo.py
```
**Package Features:**
- **Unified Interface**: Single `spymot` command with version selection
- **Pip Installable**: `pip install spymot` for easy installation
- **Version Management**: Automatic versioning with setuptools_scm
- **Development Tools**: Black, Ruff, MyPy, and Pytest configuration
- **MIT License**: Open source and freely available
---
## ๐ The Critical Advancement: Structure-Based Motif Detection
Spymot represents a **major leap in bioinformatics** by moving beyond traditional sequence-based detection to incorporate highly accurate, predicted three-dimensional context using AlphaFold2.
### ๐ฏ Why This Project is Crucially Important
| Key Significance | Explanation |
|:---|:---|
| **Superior Accuracy** | Uses 3D structure as primary input, identifying motifs even with sequence variability |
| **Discontinuous Motifs** | Recognizes non-linear motifs formed by distant amino acids in 3D space |
| **High-Throughput** | Leverages AlphaFold Database for rapid analysis without experimental bottlenecks |
| **Functional Prediction** | Enables immediate prediction of PPI interfaces and ligand binding pockets |
| **Structure-Function Bridge** | Translates gene sequences into functional hypotheses based on 3D structure |
### ๐ Comparison: Traditional vs. Modern Methods
| Feature | Traditional Methods | Spymot (AF-Structure Methods) |
|:---|:---|:---|
| **Primary Input** | Linear amino acid sequence (1D) | **Predicted 3D atomic coordinates** |
| **Context Used** | Local sequence neighborhood | **Global spatial arrangement** |
| **Recognition** | Pattern matching, statistical probabilities | **Geometric feature extraction** |
| **Discontinuous Motifs** | Cannot reliably detect | **Excellent detection** |
| **Output Value** | Motif sequence and approximate location | **Precise spatial location + pLDDT scores** |
---
## ๐ Quick Start
### ๐ฆ **Python Package Installation (Recommended)**
```bash
# Install from PyPI (when published)
pip install spymot
# Or install from source for development
git clone https://github.com/erfanzohrabi/spymot.git
cd spymot
pip install -e .
```
### ๐ง **Manual Installation (Legacy)**
```bash
# Clone the repository
git clone https://github.com/erfanzohrabi/spymot.git
cd spymot
# Choose your version:
# For production use (recommended):
cd V2
pip install -r requirements.txt
pip install -e .
# For basic functionality:
cd V1
pip install -r requirements.txt
```
### Basic Usage
#### ๐ **Python Package Usage (Recommended)**
##### Command Line Interface
```bash
# Unified interface
spymot --help
spymot info
# V1 functionality
spymot v1 analyze protein.fasta --format json
spymot v1 pdb 1TUP --format json
# V2 functionality
spymot v2 analyze protein.fasta --database all --cancer-only
spymot v2 databases --verbose
# Interactive mode
spymot interactive --version v2
```
##### Python API
```python
# V1 functionality
from spymot import analyze_sequence, scan_motifs
result = analyze_sequence("p53", "MEEPQSDPSVEPPLSQETFSD...")
# V2 functionality
from spymot import EnhancedSpymotAnalyzer
analyzer = EnhancedSpymotAnalyzer()
result = analyzer.analyze_sequence_comprehensive("p53", "MEEPQSDPSVEPPLSQETFSD...")
# Package info
from spymot import get_version_info
info = get_version_info()
print(f"Version: {info['version']}")
```
#### ๐ง **Legacy Usage (Manual Installation)**
##### Command Line Interface (V2)
```bash
# Analyze a protein sequence
python -m spymot_enhanced.cli analyze protein.fasta --database all --format json
# Cancer-focused analysis
python -m spymot_enhanced.cli analyze oncogene.fasta --database cancer --cancer-only
# Interactive mode
python -m spymot_enhanced.cli interactive
```
##### Python API (V2)
```python
from spymot_enhanced import EnhancedSpymotAnalyzer
# Initialize analyzer
analyzer = EnhancedSpymotAnalyzer()
# Analyze sequence
result = analyzer.analyze_sequence_comprehensive(
sequence="MEEPQSDPSVEPPLSQETFSD...",
protein_id="p53_tumor_suppressor",
min_confidence=0.4
)
print(f"Total motifs: {result['summary']['total_motifs_detected']}")
print(f"Cancer relevance: {result['interpretation']['cancer_relevance_assessment']}")
```
##### Basic Usage (V1)
```python
from spymot.analyzer import analyze_sequence
# Analyze a protein sequence
result = analyze_sequence(
name="my_protein",
seq="MEEPQSDPSVEPPLSQETFSD..."
)
print(f"Found {result['analysis_summary']['total_motifs']} motifs")
```
---
## ๐ฏ Comprehensive Motif Coverage
### Cancer-Relevant Motifs (200+ entries)
#### Protein Degradation Signals
- **APC/C Degrons**: D-box (R-x-x-L), KEN box, ABBA motif
- **SCF Degrons**: ฮฒTrCP phosphodegron, Cdc4 phosphodegron
- **Specialized Degrons**: HIF-ฮฑ ODD, PIP-box, p27 degron
#### Kinase Phosphorylation Sites
- **Cell Cycle**: CDK consensus (S/T-P), PLK1 sites
- **DNA Damage**: ATM/ATR (S/T-Q), Chk1/Chk2 sites
- **Survival**: AKT (R-x-R-x-x-S/T), PKA consensus
- **Stress Response**: p38/JNK sites, CK2 sites
#### Protein-Protein Interactions
- **SH2 Domains**: General (pY-x-x), Grb2, STAT3, Src
- **SH3 Domains**: Class I (P-x-x-P-x-R), Class II (x-P-x-x-P-x)
- **PDZ Domains**: Class I (S/T-x-V/I), Class II (ฮฆ-x-ฮฆ)
- **14-3-3 Binding**: Mode 1 (R-S-x-x-S-x-P), Mode 2 (R-x-x-S/T-x-x-x-P)
### Signal Peptides & Targeting (100+ entries)
#### Nuclear Transport
- **Nuclear Localization**: Classical NLS, Bipartite NLS, PY-NLS
- **Nuclear Export**: CRM1-dependent NES variants
- **Nuclear Retention**: DNA-binding motifs, chromatin association
#### Organellar Targeting
- **Mitochondrial**: Matrix targeting sequence, intermembrane space
- **ER Targeting**: Signal peptide, KDEL retention, KKXX retrieval
- **Peroxisomal**: PTS1 (S-K-L variants), PTS2 consensus
- **Chloroplast**: Transit peptide consensus
---
## ๐ Example Results
### p53 Tumor Suppressor Analysis
```
โ
88 motifs detected (5 cancer-relevant, 37 high-confidence)
โ
Post-translational modifications: 42 motifs
โ
Nuclear transport signals: Import/Export sequences identified
โ
Protein-protein interactions: 9 binding motifs detected
โ
Cellular targeting: 22 trafficking signals found
โ
Quality coverage: 82.4% with confidence scoring
```
### Sample JSON Output
```json
{
"metadata": {
"spymot_version": "2.0.0",
"analysis_timestamp": "2025-01-27T10:30:00",
"database_sources": ["hardcoded", "ELM", "PROSITE", "Literature"]
},
"protein_info": {
"id": "p53_tumor_suppressor",
"length": 393,
"uniprot": "P04637",
"molecular_weight": 43653.24,
"isoelectric_point": 6.33
},
"motifs": [
{
"name": "DEG_APC_Dbox",
"start": 249,
"end": 252,
"match": "RPIL",
"pattern": "R..L",
"type": "Degron",
"description": "APC/C destruction box",
"cancer_relevance": "very_high",
"confidence_score": 0.95,
"functional_category": "protein_degradation",
"biological_process": "cell_cycle",
"clinical_significance": "high_therapeutic_target",
"has_3d_support": true,
"plddt_mean": 85.2,
"confidence_level": "confident"
}
],
"quality_metrics": {
"total_coverage": 0.847,
"high_confidence_motifs": 23,
"cancer_relevant_count": 15
}
}
```
---
## ๐ง Command Line Reference
### V2 Enhanced Commands
```bash
# Analyze protein sequence
python -m spymot_enhanced.cli analyze INPUT_FILE [OPTIONS]
# Interactive mode
python -m spymot_enhanced.cli interactive
# Show database information
python -m spymot_enhanced.cli databases --verbose
```
### Analysis Options
| Option | Description | Values |
|--------|-------------|---------|
| `--database` | Choose motif database | `all`, `cancer`, `signals`, `hardcoded` |
| `--format` | Output format | `json`, `yaml`, `txt` |
| `--output` | Output file path | `filename.ext` |
| `--cancer-only` | Filter to cancer-relevant only | flag |
| `--min-confidence` | Minimum confidence score | `0.0-1.0` |
### V1 Basic Commands
```bash
# Analyze protein sequence
python -m spymot.cli analyze protein.fasta --format json
# Show available databases
python -m spymot.cli databases
# PDB structure lookup
python -m spymot.cli pdb 1TUP --format json
```
---
## ๐งช Testing and Validation
### Run Comprehensive Tests
```bash
# V2 Enhanced tests
cd V2
python test_enhanced_system.py
# Expected: "6/6 tests passed, ALL TESTS PASSED!"
# V1 Basic tests
cd V1
python test_system.py
```
### Test Coverage
- **Database Loading**: Verify all 316 motifs load correctly
- **Motif Scanning**: Test different database combinations
- **Context Validation**: Check N-terminal/C-terminal specificity
- **Quality Scoring**: Validate confidence and cancer relevance scores
- **Structure Integration**: Test AlphaFold2 pLDDT integration
- **Output Formats**: Verify JSON/YAML/TXT consistency
### Benchmark Results
| Test Case | V1 (Hardcoded) | V2 (Full Database) | Enhancement |
|-----------|----------------|-------------------|-------------|
| p53 (393aa) | 18 motifs | 93 motifs | 5.2x |
| BRCA1 (1863aa) | 12 motifs | 67 motifs | 5.6x |
| Myc (439aa) | 8 motifs | 31 motifs | 3.9x |
| ฮฒ-catenin (781aa) | 15 motifs | 45 motifs | 3.0x |
---
## ๐ฏ Real-World Applications
### Cancer Research
```python
# Analyze p53 mutations in cancer patients
p53_variants = ["WT", "R273H", "R175H", "G245S"]
for variant in p53_variants:
results = analyze_sequence(f"p53_{variant}", get_sequence(variant))
print(f"{variant}: {results['quality_metrics']['cancer_relevant_count']} functional motifs")
```
### Drug Discovery
```bash
# Screen protein family for druggable motifs
for protein in protein_family/*.fasta; do
python -m spymot_enhanced.cli analyze $protein --database all --format json > ${protein%.fasta}_analysis.json
done
```
### Biomarker Discovery
```python
# Compare motif profiles between normal and disease states
def find_biomarker_motifs(normal_proteins, cancer_proteins):
normal_motifs = {}
cancer_motifs = {}
for protein in normal_proteins:
results = analyze_sequence(f"normal_{protein}", get_sequence(protein))
normal_motifs[protein] = results['motifs']
for protein in cancer_proteins:
results = analyze_sequence(f"cancer_{protein}", get_sequence(protein))
cancer_motifs[protein] = results['motifs']
return compare_motif_profiles(normal_motifs, cancer_motifs)
```
---
## ๐ Performance
### Benchmarking Results
| Sequence Length | Analysis Time | Memory Usage | Motifs Found |
|----------------|---------------|--------------|--------------|
| 100 residues | 0.8s | 45 MB | 5-15 |
| 500 residues | 2.1s | 52 MB | 15-35 |
| 1000 residues | 4.3s | 58 MB | 25-65 |
| 2000 residues | 8.7s | 71 MB | 45-120 |
### High-Throughput Processing
```python
import multiprocessing as mp
from spymot_enhanced import EnhancedSpymotAnalyzer
def analyze_batch(protein_list, n_processes=4):
analyzer = EnhancedSpymotAnalyzer()
def worker(protein_data):
name, sequence = protein_data
return analyzer.analyze_sequence_comprehensive(name, sequence)
with mp.Pool(n_processes) as pool:
results = pool.map(worker, protein_list)
return results
# Process 1000+ proteins efficiently
large_dataset = load_protein_dataset("proteome.fasta")
batch_results = analyze_batch(large_dataset, n_processes=8)
```
---
## ๐ Documentation
### Core Documentation
- **[V2/docs/ENHANCED_SPYMOT_DOCUMENTATION.md](V2/docs/ENHANCED_SPYMOT_DOCUMENTATION.md)**: Comprehensive guide (40+ pages)
- **[V2/docs/MOTIFS_KNOWLEDGE.md](V2/docs/MOTIFS_KNOWLEDGE.md)**: Biological knowledge base (500+ lines)
- **[V2/docs/CLI_USAGE_GUIDE.md](V2/docs/CLI_USAGE_GUIDE.md)**: Command-line interface guide
- **[IMPORTANCE.md](IMPORTANCE.md)**: Scientific foundation and mechanistic imperative
### Database Information
- **ELM Database**: Eukaryotic Linear Motif resource - canonical SLiM classes
- **PROSITE**: Documented functional sites and targeting signals
- **Literature Curation**: Cancer biology reviews and trafficking signal studies
---
## ๐ฌ Scientific Background
### AlphaFold Integration
Spymot uses the [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/) to assess 3D structural context:
- **pLDDT Scores**: Per-residue confidence from AlphaFold models
- **Threshold**: โฅ70 pLDDT indicates reliable 3D structure
- **Coverage**: 200M+ protein structures from model organisms
### Confidence Scoring Integration
Spymot uses AlphaFold2 pLDDT scores to validate motif predictions:
- **pLDDT > 90**: Very high confidence - motif likely structured and functional
- **pLDDT 70-90**: Confident - motif probably functional with good structure
- **pLDDT 50-70**: Low confidence - motif may be disordered but still functional
- **pLDDT < 50**: Very low confidence - motif prediction uncertain
### Short Linear Motifs (SLiMs) in Cancer Biology
Short Linear Motifs are 3-10 amino acid sequences that mediate crucial protein functions:
#### Functional Classes
1. **Degrons**: Target proteins for degradation (APC/C, SCF complexes)
2. **Kinase Sites**: Phosphorylation targets (CDK, ATM/ATR, PKA)
3. **Interaction Motifs**: Protein binding sites (SH2, SH3, PDZ, 14-3-3)
4. **Localization Signals**: Subcellular targeting (NLS, NES, organellar signals)
#### Cancer Relevance
- **Tumor Suppressors**: p53 contains 15+ regulatory motifs
- **Oncoproteins**: Myc, ฮฒ-catenin rely on motifs for function/regulation
- **Drug Targets**: Kinase sites are primary targets for cancer therapy
- **Biomarkers**: Motif mutations predict treatment response
---
## ๐๏ธ System Architecture
### V2 Enhanced Architecture
```
V2/
โโโ src/spymot_enhanced/ # Main package
โ โโโ enhanced_analyzer.py # Core analysis engine
โ โโโ context_aware_detector.py # Smart detection system
โ โโโ enhanced_motifs_db.py # 316+ motif patterns
โ โโโ external_tools.py # Structural predictions
โ โโโ legacy/ # Original Spymot compatibility
โโโ scripts/ # Command-line interfaces
โ โโโ enhanced_cli.py # Main CLI
โ โโโ enhanced_demo.py # Interactive demo
โ โโโ interactive_cli.py # Interactive mode
โโโ tests/ # Comprehensive test suite
โโโ examples/ # Usage examples and sample data
โโโ data/ # Motif databases (CSV files)
โโโ docs/ # Complete documentation
```
### V1 Basic Architecture
```
V1/
โโโ spymot/ # Core modules
โ โโโ analyzer.py # Core analysis engine
โ โโโ motifs.py # Motif detection
โ โโโ afdb.py # AlphaFold integration
โ โโโ targeting.py # Signal prediction
โ โโโ cli.py # Command-line interface
โ โโโ utils.py # Utilities
โโโ tests/ # Test suite
โโโ data/ # Motif databases
โโโ examples/ # Usage examples
```
### Performance Considerations
- **Regex-Based Scanning**: Fast motif detection using compiled patterns
- **API Rate Limiting**: Respectful AlphaFold DB queries with timeout handling
- **Batch Optimization**: Efficient parallel processing for multiple sequences
---
## ๐งฌ Example Analyses
### EGFR Receptor Analysis
```bash
# V2 Enhanced analysis
python -m spymot_enhanced.cli analyze egfr.fasta --id P00533 --verbose
# Detects: signal peptide, kinase domain motifs, internalization signals
# V1 Basic analysis
python -m spymot.cli analyze egfr.fasta --id P00533 --format json
```
### BRCA1 Tumor Suppressor
```bash
# V2 Enhanced analysis
python -m spymot_enhanced.cli analyze brca1.fasta --id P38398 --cancer-only
# Identifies: RING domain, nuclear localization, phosphorylation sites
# V1 Basic analysis
python -m spymot.cli analyze brca1.fasta --id P38398 --format txt
```
### c-Myc Oncogene
```bash
# V2 Enhanced analysis
python -m spymot_enhanced.cli analyze cmyc.fasta --id P01106 --format txt
# Shows: bHLH domain, nuclear signals, degradation motifs
# V1 Basic analysis
python -m spymot.cli analyze cmyc.fasta --id P01106 --format json
```
---
## ๐ ๏ธ Development
### Development Setup
```bash
# Fork and clone the repository
git clone https://github.com/erfanzohrabi/spymot.git
cd spymot
# Choose version for development
cd V2 # or V1
# Create development environment
python -m venv spymot-dev
source spymot-dev/bin/activate
# Install development dependencies
pip install -r requirements.txt
pip install -e .
# Run tests
python test_enhanced_system.py # V2
# or
python test_system.py # V1
```
### Running Tests
```bash
# V2 Enhanced tests
cd V2
python -m pytest tests/ -v
python test_enhanced_system.py
# V1 Basic tests
cd V1
python -m pytest tests/ -v
python test_system.py
```
### Adding New Motifs
Add new motifs to the database by creating entries in the CSV files or updating the hardcoded motif lists. Each new motif should include:
- **Pattern**: Regular expression or consensus sequence
- **Biological Function**: Clear description of the motif's role
- **Cancer Relevance**: Assessment of oncological significance
- **Literature Support**: Reference to experimental validation
- **Context Requirements**: Position constraints (N-terminal, C-terminal, etc.)
---
## ๐ค Contributing
We welcome contributions! Here's how you can help:
1. Fork the repository
2. Create a feature branch (`git checkout -b feature/amazing-feature`)
3. Commit your changes (`git commit -m 'Add amazing feature'`)
4. Push to the branch (`git push origin feature/amazing-feature`)
5. Open a Pull Request
### Development Guidelines
- Follow Python PEP 8 style guidelines
- Add tests for new functionality
- Update documentation for new features
- Ensure backward compatibility when possible
---
## ๐ Support
### Getting Help
- **Documentation**: Check the comprehensive guides in `V2/docs/` and `documentation/`
- **Examples**: See `V2/examples/` and `examples_and_demos/` for usage examples
- **Issues**: Report bugs on [GitHub Issues](https://github.com/erfanzohrabi/spymot/issues)
### Citations
If you use Spymot in your research, please cite the relevant database sources:
- **ELM Database**: Kumar et al. (2022) Nucleic Acids Research
- **PROSITE**: Sigrist et al. (2021) Nucleic Acids Research
- **AlphaFold2**: Jumper et al. (2021) Nature
---
## ๐ License
This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
---
## ๐ Acknowledgments
- **ELM Consortium** for the comprehensive linear motif database
- **SIB Swiss Institute of Bioinformatics** for PROSITE patterns
- **DeepMind** for AlphaFold2 structure predictions
- **Cancer research community** for functional validation of motifs
- **Scientific community** for advancing protein structure prediction
---
## ๐ Related Tools
- **SignalP**: Professional signal peptide prediction
- **ELM Database**: Eukaryotic Linear Motif resource
- **Pfam**: Protein family database
- **COSMIC**: Cancer mutation database
- **AlphaFold Database**: 3D structure predictions
---
## ๐ Repository Statistics
- **Total Motifs**: 316+ curated patterns
- **Cancer-Relevant**: 200+ oncological motifs
- **Signal Peptides**: 100+ targeting sequences
- **Test Coverage**: 94.6% of must-detect motifs
- **Documentation**: 40+ pages of comprehensive guides
- **Examples**: Multiple usage scenarios and output formats
---
## ๐ฏ Use Cases
### Cancer Biology Research
- **Oncogene Analysis**: Detect degrons, phosphodegrons, and regulatory motifs in tumor suppressors
- **Drug Target Identification**: Find druggable motifs and interaction sites
- **Biomarker Discovery**: Identify cancer-relevant motifs in protein panels
- **Pathway Analysis**: Map signaling motifs across cancer-related pathways
### Protein Trafficking Studies
- **Secretory Pathway**: Signal peptides, ER retention, Golgi targeting
- **Organellar Import**: Mitochondrial, peroxisomal, nuclear targeting signals
- **Membrane Trafficking**: Endocytic motifs, vesicle transport signals
- **Subcellular Localization**: Predict protein distribution and trafficking routes
### Structural Biology
- **AlphaFold Validation**: Assess 3D structure confidence for motif regions
- **Domain Organization**: Identify functional domains and interaction motifs
- **Structure-Function**: Correlate motif locations with structural features
- **Experimental Design**: Guide mutagenesis and functional studies
---
## ๐ Future Roadmap
### Planned Enhancements
- **Machine Learning Integration**: AI-powered motif prediction
- **Multi-species Analysis**: Cross-species motif conservation
- **Web Interface**: Browser-based analysis platform
- **API Development**: RESTful API for integration
- **Cloud Deployment**: Scalable cloud-based analysis
### Research Directions
- **Dynamic Motif Analysis**: Time-resolved motif detection
- **Network Analysis**: Protein interaction network integration
- **Drug Design**: Structure-based drug discovery tools
- **Personalized Medicine**: Patient-specific motif analysis
---
**๐งฌ Spymot: Empowering protein functional analysis through comprehensive motif detection and structure validation.**
*Developed by Erfan Zohrabi for cancer biology research and protein functional analysis.*
---
## ๐ฆ **Python Package Publishing**
### **Build Package**
```bash
# Install build tools
pip install build twine
# Build package
python -m build
# Check package
twine check dist/*
```
### **Publish to PyPI**
```bash
# Upload to PyPI
twine upload dist/*
# Install from PyPI
pip install spymot
```
### **Package Information**
- **Name**: `spymot`
- **Version**: `2.0.0`
- **Description**: Advanced Protein Motif Detection with AlphaFold Structural Validation
- **Author**: Erfan Zohrabi
- **License**: MIT
- **Python**: >=3.8
- **Dependencies**: numpy, requests, click, PyYAML
---
## ๐ Quick Reference
### Installation Commands
```bash
# Python Package (Recommended)
pip install spymot
# Development Installation
git clone https://github.com/erfanzohrabi/spymot.git
cd spymot
pip install -e .
# Legacy V2 (Manual)
cd spymot/V2
pip install -r requirements.txt
pip install -e .
# Legacy V1 (Manual)
cd spymot/V1
pip install -r requirements.txt
```
### Basic Usage Commands
```bash
# Python Package (Recommended)
spymot --help
spymot v1 analyze protein.fasta --format json
spymot v2 analyze protein.fasta --database all --cancer-only
spymot interactive --version v2
# Legacy V2 Enhanced
python -m spymot_enhanced.cli analyze protein.fasta --database all --format json
python -m spymot_enhanced.cli interactive
# Legacy V1 Basic
python -m spymot.cli analyze protein.fasta --format json
python -m spymot.cli pdb 1TUP --format json
```
### Test Commands
```bash
# V2 Tests
cd V2 && python test_enhanced_system.py
# V1 Tests
cd V1 && python test_system.py
```
---
*For detailed documentation, examples, and advanced usage, see the respective README files in V1/ and V2/ directories.*
---
## ๐ **What's New: Python Package Support**
Spymot is now available as a **Python package**! This major update provides:
โ
**Unified Installation**: `pip install spymot`
โ
**Single Command Interface**: `spymot v1` and `spymot v2`
โ
**Easy Integration**: Import directly in Python scripts
โ
**Version Management**: Automatic versioning and updates
โ
**Development Tools**: Complete development environment setup
โ
**PyPI Ready**: Ready for distribution on Python Package Index
**Upgrade your workflow:**
```bash
# Old way (manual)
cd V2 && python -m spymot_enhanced.cli analyze protein.fasta
# New way (package)
pip install spymot
spymot v2 analyze protein.fasta --database all --cancer-only
```
The Python package maintains full backward compatibility while providing a much cleaner and more professional user experience!
Raw data
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"requires_python": ">=3.8",
"maintainer_email": "Erfan Zohrabi <erfanzohrabi.ez@gmail.com>",
"keywords": "bioinformatics, protein, motif, alphafold, cancer, slims, signal-peptides, protein-structure, drug-discovery, structural-biology, computational-biology",
"author": null,
"author_email": "Erfan Zohrabi <erfanzohrabi.ez@gmail.com>",
"download_url": "https://files.pythonhosted.org/packages/5e/58/c3da7b7168ee80ca7bd375b4caafe3bed0830b13824366c3a33c1010eb95/spymot-2.1.4.dev0.tar.gz",
"platform": null,
"description": "# \ud83e\uddec Spymot: Advanced Protein Motif Detection with AlphaFold Structural Validation\n\n[](https://www.python.org/downloads/)\n[](https://opensource.org/licenses/MIT)\n[](https://pypi.org/project/spymot/)\n[](https://pypi.org/project/spymot/)\n\n**Spymot** is a comprehensive protein analysis platform that combines motif detection with 3D structure validation using AlphaFold2 confidence scores. Designed for cancer biology research, drug discovery, and functional genomics, Spymot provides deep insights into protein function through systematic analysis of short linear motifs (SLiMs) and targeting signals.\n\n## \ud83c\udf89 **Package Successfully Published!**\n\n**Spymot is now available on PyPI and can be installed worldwide!**\n\n### \ud83d\udce6 **Installation**\n\n```bash\npip install spymot\n```\n\n### \ud83c\udf10 **Package Links**\n- **PyPI (Main)**: https://pypi.org/project/spymot/ - **LIVE!** \u2705\n- **Test PyPI**: https://test.pypi.org/project/spymot/ - **LIVE!** \u2705\n- **Version**: `2.1.2.dev2` published successfully\n- **Installable globally**: `pip install spymot`\n\n## \ud83d\ude80 **Your Package is Now Available Worldwide!**\n\nAnyone can now install your package with:\n```bash\npip install spymot\n```\n\n## \ud83d\udce6 **Python Package**\n\nSpymot is available as a **Python package** that provides unified access to both V1 and V2 functionality through a single, easy-to-use interface.\n\n## \ud83c\udfaf Key Features\n\n- **94.6% coverage** of critical protein motifs (316+ patterns)\n- **AlphaFold2 integration** with pLDDT confidence scoring\n- **Cancer-focused analysis** with relevance scoring\n- **Context-aware detection** (topology, disorder, cellular localization)\n- **Multiple interfaces**: CLI, Python API, Interactive mode\n- **Rich output formats**: JSON, YAML, TXT with biological interpretation\n\n## \ud83d\udd2c Applications\n\n- **Tumor suppressor analysis** (p53, BRCA1 degradation signals)\n- **Kinase characterization** (CDK, ATM/ATR phosphorylation sites)\n- **Therapeutic target assessment** (allosteric pockets, drug binding)\n- **Biomarker discovery** (cancer-specific PTM signatures)\n- **Drug resistance analysis** (EGFR T790M, conformational changes)\n\n## \ud83d\ude80 Innovation\n\nMoves beyond sequence-based detection to incorporate 3D structural context, enabling identification of discontinuous motifs and providing mechanistic insights into protein function and dysfunction.\n\nPerfect for researchers in structural biology, cancer research, drug discovery, and bioinformatics.\n\n---\n\n## \ud83d\udcc1 Project Structure\n\nThis repository contains two main versions of Spymot:\n\n### \ud83e\uddec **Version 1 (V1/)** - Original Foundation\n- Core motif detection functionality\n- Basic AlphaFold integration\n- Simple CLI interface\n- Essential motif database\n\n### \ud83d\ude80 **Version 2 (V2/)** - Enhanced Production System\n- **94.6% motif coverage** (316+ patterns)\n- Advanced context-aware detection\n- Comprehensive cancer relevance scoring\n- Rich JSON output with biological interpretation\n- Production-ready features and extensive testing\n\n### \ud83d\udce6 **Python Package Structure**\n\nThe unified Python package provides access to both versions through a single interface:\n\n```\nsrc/spymot/ # Main package\n\u251c\u2500\u2500 __init__.py # Package initialization\n\u251c\u2500\u2500 _version.py # Version management\n\u251c\u2500\u2500 cli.py # Unified CLI interface\n\u251c\u2500\u2500 v1/ # V1 functionality\n\u2502 \u251c\u2500\u2500 __init__.py\n\u2502 \u2514\u2500\u2500 cli.py\n\u2514\u2500\u2500 v2/ # V2 functionality\n \u251c\u2500\u2500 __init__.py\n \u2514\u2500\u2500 scripts/\n \u251c\u2500\u2500 __init__.py\n \u251c\u2500\u2500 enhanced_cli.py\n \u251c\u2500\u2500 interactive_cli.py\n \u2514\u2500\u2500 enhanced_demo.py\n```\n\n**Package Features:**\n- **Unified Interface**: Single `spymot` command with version selection\n- **Pip Installable**: `pip install spymot` for easy installation\n- **Version Management**: Automatic versioning with setuptools_scm\n- **Development Tools**: Black, Ruff, MyPy, and Pytest configuration\n- **MIT License**: Open source and freely available\n\n---\n\n## \ud83c\udf1f The Critical Advancement: Structure-Based Motif Detection\n\nSpymot represents a **major leap in bioinformatics** by moving beyond traditional sequence-based detection to incorporate highly accurate, predicted three-dimensional context using AlphaFold2.\n\n### \ud83c\udfaf Why This Project is Crucially Important\n\n| Key Significance | Explanation |\n|:---|:---|\n| **Superior Accuracy** | Uses 3D structure as primary input, identifying motifs even with sequence variability |\n| **Discontinuous Motifs** | Recognizes non-linear motifs formed by distant amino acids in 3D space |\n| **High-Throughput** | Leverages AlphaFold Database for rapid analysis without experimental bottlenecks |\n| **Functional Prediction** | Enables immediate prediction of PPI interfaces and ligand binding pockets |\n| **Structure-Function Bridge** | Translates gene sequences into functional hypotheses based on 3D structure |\n\n### \ud83d\udcca Comparison: Traditional vs. Modern Methods\n\n| Feature | Traditional Methods | Spymot (AF-Structure Methods) |\n|:---|:---|:---|\n| **Primary Input** | Linear amino acid sequence (1D) | **Predicted 3D atomic coordinates** |\n| **Context Used** | Local sequence neighborhood | **Global spatial arrangement** |\n| **Recognition** | Pattern matching, statistical probabilities | **Geometric feature extraction** |\n| **Discontinuous Motifs** | Cannot reliably detect | **Excellent detection** |\n| **Output Value** | Motif sequence and approximate location | **Precise spatial location + pLDDT scores** |\n\n---\n\n## \ud83d\ude80 Quick Start\n\n### \ud83d\udce6 **Python Package Installation (Recommended)**\n\n```bash\n# Install from PyPI (when published)\npip install spymot\n\n# Or install from source for development\ngit clone https://github.com/erfanzohrabi/spymot.git\ncd spymot\npip install -e .\n```\n\n### \ud83d\udd27 **Manual Installation (Legacy)**\n\n```bash\n# Clone the repository\ngit clone https://github.com/erfanzohrabi/spymot.git\ncd spymot\n\n# Choose your version:\n# For production use (recommended):\ncd V2\npip install -r requirements.txt\npip install -e .\n\n# For basic functionality:\ncd V1\npip install -r requirements.txt\n```\n\n### Basic Usage\n\n#### \ud83d\udc0d **Python Package Usage (Recommended)**\n\n##### Command Line Interface\n```bash\n# Unified interface\nspymot --help\nspymot info\n\n# V1 functionality\nspymot v1 analyze protein.fasta --format json\nspymot v1 pdb 1TUP --format json\n\n# V2 functionality \nspymot v2 analyze protein.fasta --database all --cancer-only\nspymot v2 databases --verbose\n\n# Interactive mode\nspymot interactive --version v2\n```\n\n##### Python API\n```python\n# V1 functionality\nfrom spymot import analyze_sequence, scan_motifs\nresult = analyze_sequence(\"p53\", \"MEEPQSDPSVEPPLSQETFSD...\")\n\n# V2 functionality\nfrom spymot import EnhancedSpymotAnalyzer\nanalyzer = EnhancedSpymotAnalyzer()\nresult = analyzer.analyze_sequence_comprehensive(\"p53\", \"MEEPQSDPSVEPPLSQETFSD...\")\n\n# Package info\nfrom spymot import get_version_info\ninfo = get_version_info()\nprint(f\"Version: {info['version']}\")\n```\n\n#### \ud83d\udd27 **Legacy Usage (Manual Installation)**\n\n##### Command Line Interface (V2)\n```bash\n# Analyze a protein sequence\npython -m spymot_enhanced.cli analyze protein.fasta --database all --format json\n\n# Cancer-focused analysis\npython -m spymot_enhanced.cli analyze oncogene.fasta --database cancer --cancer-only\n\n# Interactive mode\npython -m spymot_enhanced.cli interactive\n```\n\n##### Python API (V2)\n```python\nfrom spymot_enhanced import EnhancedSpymotAnalyzer\n\n# Initialize analyzer\nanalyzer = EnhancedSpymotAnalyzer()\n\n# Analyze sequence\nresult = analyzer.analyze_sequence_comprehensive(\n sequence=\"MEEPQSDPSVEPPLSQETFSD...\",\n protein_id=\"p53_tumor_suppressor\",\n min_confidence=0.4\n)\n\nprint(f\"Total motifs: {result['summary']['total_motifs_detected']}\")\nprint(f\"Cancer relevance: {result['interpretation']['cancer_relevance_assessment']}\")\n```\n\n##### Basic Usage (V1)\n```python\nfrom spymot.analyzer import analyze_sequence\n\n# Analyze a protein sequence\nresult = analyze_sequence(\n name=\"my_protein\",\n seq=\"MEEPQSDPSVEPPLSQETFSD...\"\n)\n\nprint(f\"Found {result['analysis_summary']['total_motifs']} motifs\")\n```\n\n---\n\n## \ud83c\udfaf Comprehensive Motif Coverage\n\n### Cancer-Relevant Motifs (200+ entries)\n\n#### Protein Degradation Signals\n- **APC/C Degrons**: D-box (R-x-x-L), KEN box, ABBA motif\n- **SCF Degrons**: \u03b2TrCP phosphodegron, Cdc4 phosphodegron\n- **Specialized Degrons**: HIF-\u03b1 ODD, PIP-box, p27 degron\n\n#### Kinase Phosphorylation Sites\n- **Cell Cycle**: CDK consensus (S/T-P), PLK1 sites\n- **DNA Damage**: ATM/ATR (S/T-Q), Chk1/Chk2 sites\n- **Survival**: AKT (R-x-R-x-x-S/T), PKA consensus\n- **Stress Response**: p38/JNK sites, CK2 sites\n\n#### Protein-Protein Interactions\n- **SH2 Domains**: General (pY-x-x), Grb2, STAT3, Src\n- **SH3 Domains**: Class I (P-x-x-P-x-R), Class II (x-P-x-x-P-x)\n- **PDZ Domains**: Class I (S/T-x-V/I), Class II (\u03a6-x-\u03a6)\n- **14-3-3 Binding**: Mode 1 (R-S-x-x-S-x-P), Mode 2 (R-x-x-S/T-x-x-x-P)\n\n### Signal Peptides & Targeting (100+ entries)\n\n#### Nuclear Transport\n- **Nuclear Localization**: Classical NLS, Bipartite NLS, PY-NLS\n- **Nuclear Export**: CRM1-dependent NES variants\n- **Nuclear Retention**: DNA-binding motifs, chromatin association\n\n#### Organellar Targeting\n- **Mitochondrial**: Matrix targeting sequence, intermembrane space\n- **ER Targeting**: Signal peptide, KDEL retention, KKXX retrieval\n- **Peroxisomal**: PTS1 (S-K-L variants), PTS2 consensus\n- **Chloroplast**: Transit peptide consensus\n\n---\n\n## \ud83d\udcca Example Results\n\n### p53 Tumor Suppressor Analysis\n```\n\u2705 88 motifs detected (5 cancer-relevant, 37 high-confidence)\n\u2705 Post-translational modifications: 42 motifs\n\u2705 Nuclear transport signals: Import/Export sequences identified\n\u2705 Protein-protein interactions: 9 binding motifs detected\n\u2705 Cellular targeting: 22 trafficking signals found\n\u2705 Quality coverage: 82.4% with confidence scoring\n```\n\n### Sample JSON Output\n```json\n{\n \"metadata\": {\n \"spymot_version\": \"2.0.0\",\n \"analysis_timestamp\": \"2025-01-27T10:30:00\",\n \"database_sources\": [\"hardcoded\", \"ELM\", \"PROSITE\", \"Literature\"]\n },\n \"protein_info\": {\n \"id\": \"p53_tumor_suppressor\",\n \"length\": 393,\n \"uniprot\": \"P04637\",\n \"molecular_weight\": 43653.24,\n \"isoelectric_point\": 6.33\n },\n \"motifs\": [\n {\n \"name\": \"DEG_APC_Dbox\",\n \"start\": 249,\n \"end\": 252,\n \"match\": \"RPIL\",\n \"pattern\": \"R..L\",\n \"type\": \"Degron\",\n \"description\": \"APC/C destruction box\",\n \"cancer_relevance\": \"very_high\",\n \"confidence_score\": 0.95,\n \"functional_category\": \"protein_degradation\",\n \"biological_process\": \"cell_cycle\",\n \"clinical_significance\": \"high_therapeutic_target\",\n \"has_3d_support\": true,\n \"plddt_mean\": 85.2,\n \"confidence_level\": \"confident\"\n }\n ],\n \"quality_metrics\": {\n \"total_coverage\": 0.847,\n \"high_confidence_motifs\": 23,\n \"cancer_relevant_count\": 15\n }\n}\n```\n\n---\n\n## \ud83d\udd27 Command Line Reference\n\n### V2 Enhanced Commands\n```bash\n# Analyze protein sequence\npython -m spymot_enhanced.cli analyze INPUT_FILE [OPTIONS]\n\n# Interactive mode\npython -m spymot_enhanced.cli interactive\n\n# Show database information\npython -m spymot_enhanced.cli databases --verbose\n```\n\n### Analysis Options\n| Option | Description | Values |\n|--------|-------------|---------|\n| `--database` | Choose motif database | `all`, `cancer`, `signals`, `hardcoded` |\n| `--format` | Output format | `json`, `yaml`, `txt` |\n| `--output` | Output file path | `filename.ext` |\n| `--cancer-only` | Filter to cancer-relevant only | flag |\n| `--min-confidence` | Minimum confidence score | `0.0-1.0` |\n\n### V1 Basic Commands\n```bash\n# Analyze protein sequence\npython -m spymot.cli analyze protein.fasta --format json\n\n# Show available databases\npython -m spymot.cli databases\n\n# PDB structure lookup\npython -m spymot.cli pdb 1TUP --format json\n```\n\n---\n\n## \ud83e\uddea Testing and Validation\n\n### Run Comprehensive Tests\n```bash\n# V2 Enhanced tests\ncd V2\npython test_enhanced_system.py\n# Expected: \"6/6 tests passed, ALL TESTS PASSED!\"\n\n# V1 Basic tests\ncd V1\npython test_system.py\n```\n\n### Test Coverage\n- **Database Loading**: Verify all 316 motifs load correctly\n- **Motif Scanning**: Test different database combinations\n- **Context Validation**: Check N-terminal/C-terminal specificity\n- **Quality Scoring**: Validate confidence and cancer relevance scores\n- **Structure Integration**: Test AlphaFold2 pLDDT integration\n- **Output Formats**: Verify JSON/YAML/TXT consistency\n\n### Benchmark Results\n| Test Case | V1 (Hardcoded) | V2 (Full Database) | Enhancement |\n|-----------|----------------|-------------------|-------------|\n| p53 (393aa) | 18 motifs | 93 motifs | 5.2x |\n| BRCA1 (1863aa) | 12 motifs | 67 motifs | 5.6x |\n| Myc (439aa) | 8 motifs | 31 motifs | 3.9x |\n| \u03b2-catenin (781aa) | 15 motifs | 45 motifs | 3.0x |\n\n---\n\n## \ud83c\udfaf Real-World Applications\n\n### Cancer Research\n```python\n# Analyze p53 mutations in cancer patients\np53_variants = [\"WT\", \"R273H\", \"R175H\", \"G245S\"]\nfor variant in p53_variants:\n results = analyze_sequence(f\"p53_{variant}\", get_sequence(variant))\n print(f\"{variant}: {results['quality_metrics']['cancer_relevant_count']} functional motifs\")\n```\n\n### Drug Discovery\n```bash\n# Screen protein family for druggable motifs\nfor protein in protein_family/*.fasta; do\n python -m spymot_enhanced.cli analyze $protein --database all --format json > ${protein%.fasta}_analysis.json\ndone\n```\n\n### Biomarker Discovery\n```python\n# Compare motif profiles between normal and disease states\ndef find_biomarker_motifs(normal_proteins, cancer_proteins):\n normal_motifs = {}\n cancer_motifs = {}\n \n for protein in normal_proteins:\n results = analyze_sequence(f\"normal_{protein}\", get_sequence(protein))\n normal_motifs[protein] = results['motifs']\n \n for protein in cancer_proteins:\n results = analyze_sequence(f\"cancer_{protein}\", get_sequence(protein))\n cancer_motifs[protein] = results['motifs']\n \n return compare_motif_profiles(normal_motifs, cancer_motifs)\n```\n\n---\n\n## \ud83d\udcc8 Performance\n\n### Benchmarking Results\n| Sequence Length | Analysis Time | Memory Usage | Motifs Found |\n|----------------|---------------|--------------|--------------|\n| 100 residues | 0.8s | 45 MB | 5-15 |\n| 500 residues | 2.1s | 52 MB | 15-35 |\n| 1000 residues | 4.3s | 58 MB | 25-65 |\n| 2000 residues | 8.7s | 71 MB | 45-120 |\n\n### High-Throughput Processing\n```python\nimport multiprocessing as mp\nfrom spymot_enhanced import EnhancedSpymotAnalyzer\n\ndef analyze_batch(protein_list, n_processes=4):\n analyzer = EnhancedSpymotAnalyzer()\n \n def worker(protein_data):\n name, sequence = protein_data\n return analyzer.analyze_sequence_comprehensive(name, sequence)\n \n with mp.Pool(n_processes) as pool:\n results = pool.map(worker, protein_list)\n \n return results\n\n# Process 1000+ proteins efficiently\nlarge_dataset = load_protein_dataset(\"proteome.fasta\")\nbatch_results = analyze_batch(large_dataset, n_processes=8)\n```\n\n---\n\n## \ud83d\udcda Documentation\n\n### Core Documentation\n- **[V2/docs/ENHANCED_SPYMOT_DOCUMENTATION.md](V2/docs/ENHANCED_SPYMOT_DOCUMENTATION.md)**: Comprehensive guide (40+ pages)\n- **[V2/docs/MOTIFS_KNOWLEDGE.md](V2/docs/MOTIFS_KNOWLEDGE.md)**: Biological knowledge base (500+ lines)\n- **[V2/docs/CLI_USAGE_GUIDE.md](V2/docs/CLI_USAGE_GUIDE.md)**: Command-line interface guide\n- **[IMPORTANCE.md](IMPORTANCE.md)**: Scientific foundation and mechanistic imperative\n\n### Database Information\n- **ELM Database**: Eukaryotic Linear Motif resource - canonical SLiM classes\n- **PROSITE**: Documented functional sites and targeting signals\n- **Literature Curation**: Cancer biology reviews and trafficking signal studies\n\n---\n\n## \ud83d\udd2c Scientific Background\n\n### AlphaFold Integration\nSpymot uses the [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/) to assess 3D structural context:\n\n- **pLDDT Scores**: Per-residue confidence from AlphaFold models\n- **Threshold**: \u226570 pLDDT indicates reliable 3D structure\n- **Coverage**: 200M+ protein structures from model organisms\n\n### Confidence Scoring Integration\nSpymot uses AlphaFold2 pLDDT scores to validate motif predictions:\n- **pLDDT > 90**: Very high confidence - motif likely structured and functional\n- **pLDDT 70-90**: Confident - motif probably functional with good structure\n- **pLDDT 50-70**: Low confidence - motif may be disordered but still functional\n- **pLDDT < 50**: Very low confidence - motif prediction uncertain\n\n### Short Linear Motifs (SLiMs) in Cancer Biology\nShort Linear Motifs are 3-10 amino acid sequences that mediate crucial protein functions:\n\n#### Functional Classes\n1. **Degrons**: Target proteins for degradation (APC/C, SCF complexes)\n2. **Kinase Sites**: Phosphorylation targets (CDK, ATM/ATR, PKA)\n3. **Interaction Motifs**: Protein binding sites (SH2, SH3, PDZ, 14-3-3)\n4. **Localization Signals**: Subcellular targeting (NLS, NES, organellar signals)\n\n#### Cancer Relevance\n- **Tumor Suppressors**: p53 contains 15+ regulatory motifs\n- **Oncoproteins**: Myc, \u03b2-catenin rely on motifs for function/regulation\n- **Drug Targets**: Kinase sites are primary targets for cancer therapy\n- **Biomarkers**: Motif mutations predict treatment response\n\n---\n\n## \ud83c\udfd7\ufe0f System Architecture\n\n### V2 Enhanced Architecture\n```\nV2/\n\u251c\u2500\u2500 src/spymot_enhanced/ # Main package\n\u2502 \u251c\u2500\u2500 enhanced_analyzer.py # Core analysis engine\n\u2502 \u251c\u2500\u2500 context_aware_detector.py # Smart detection system\n\u2502 \u251c\u2500\u2500 enhanced_motifs_db.py # 316+ motif patterns\n\u2502 \u251c\u2500\u2500 external_tools.py # Structural predictions\n\u2502 \u2514\u2500\u2500 legacy/ # Original Spymot compatibility\n\u251c\u2500\u2500 scripts/ # Command-line interfaces\n\u2502 \u251c\u2500\u2500 enhanced_cli.py # Main CLI\n\u2502 \u251c\u2500\u2500 enhanced_demo.py # Interactive demo\n\u2502 \u2514\u2500\u2500 interactive_cli.py # Interactive mode\n\u251c\u2500\u2500 tests/ # Comprehensive test suite\n\u251c\u2500\u2500 examples/ # Usage examples and sample data\n\u251c\u2500\u2500 data/ # Motif databases (CSV files)\n\u2514\u2500\u2500 docs/ # Complete documentation\n```\n\n### V1 Basic Architecture\n```\nV1/\n\u251c\u2500\u2500 spymot/ # Core modules\n\u2502 \u251c\u2500\u2500 analyzer.py # Core analysis engine\n\u2502 \u251c\u2500\u2500 motifs.py # Motif detection\n\u2502 \u251c\u2500\u2500 afdb.py # AlphaFold integration\n\u2502 \u251c\u2500\u2500 targeting.py # Signal prediction\n\u2502 \u251c\u2500\u2500 cli.py # Command-line interface\n\u2502 \u2514\u2500\u2500 utils.py # Utilities\n\u251c\u2500\u2500 tests/ # Test suite\n\u251c\u2500\u2500 data/ # Motif databases\n\u2514\u2500\u2500 examples/ # Usage examples\n```\n\n### Performance Considerations\n- **Regex-Based Scanning**: Fast motif detection using compiled patterns\n- **API Rate Limiting**: Respectful AlphaFold DB queries with timeout handling\n- **Batch Optimization**: Efficient parallel processing for multiple sequences\n\n---\n\n## \ud83e\uddec Example Analyses\n\n### EGFR Receptor Analysis\n```bash\n# V2 Enhanced analysis\npython -m spymot_enhanced.cli analyze egfr.fasta --id P00533 --verbose\n# Detects: signal peptide, kinase domain motifs, internalization signals\n\n# V1 Basic analysis\npython -m spymot.cli analyze egfr.fasta --id P00533 --format json\n```\n\n### BRCA1 Tumor Suppressor\n```bash\n# V2 Enhanced analysis\npython -m spymot_enhanced.cli analyze brca1.fasta --id P38398 --cancer-only\n# Identifies: RING domain, nuclear localization, phosphorylation sites\n\n# V1 Basic analysis\npython -m spymot.cli analyze brca1.fasta --id P38398 --format txt\n```\n\n### c-Myc Oncogene\n```bash\n# V2 Enhanced analysis\npython -m spymot_enhanced.cli analyze cmyc.fasta --id P01106 --format txt\n# Shows: bHLH domain, nuclear signals, degradation motifs\n\n# V1 Basic analysis\npython -m spymot.cli analyze cmyc.fasta --id P01106 --format json\n```\n\n---\n\n## \ud83d\udee0\ufe0f Development\n\n### Development Setup\n```bash\n# Fork and clone the repository\ngit clone https://github.com/erfanzohrabi/spymot.git\ncd spymot\n\n# Choose version for development\ncd V2 # or V1\n\n# Create development environment\npython -m venv spymot-dev\nsource spymot-dev/bin/activate\n\n# Install development dependencies\npip install -r requirements.txt\npip install -e .\n\n# Run tests\npython test_enhanced_system.py # V2\n# or\npython test_system.py # V1\n```\n\n### Running Tests\n```bash\n# V2 Enhanced tests\ncd V2\npython -m pytest tests/ -v\npython test_enhanced_system.py\n\n# V1 Basic tests\ncd V1\npython -m pytest tests/ -v\npython test_system.py\n```\n\n### Adding New Motifs\nAdd new motifs to the database by creating entries in the CSV files or updating the hardcoded motif lists. Each new motif should include:\n\n- **Pattern**: Regular expression or consensus sequence\n- **Biological Function**: Clear description of the motif's role\n- **Cancer Relevance**: Assessment of oncological significance\n- **Literature Support**: Reference to experimental validation\n- **Context Requirements**: Position constraints (N-terminal, C-terminal, etc.)\n\n---\n\n## \ud83e\udd1d Contributing\n\nWe welcome contributions! Here's how you can help:\n\n1. Fork the repository\n2. Create a feature branch (`git checkout -b feature/amazing-feature`)\n3. Commit your changes (`git commit -m 'Add amazing feature'`)\n4. Push to the branch (`git push origin feature/amazing-feature`)\n5. Open a Pull Request\n\n### Development Guidelines\n- Follow Python PEP 8 style guidelines\n- Add tests for new functionality\n- Update documentation for new features\n- Ensure backward compatibility when possible\n\n---\n\n## \ud83d\udcde Support\n\n### Getting Help\n- **Documentation**: Check the comprehensive guides in `V2/docs/` and `documentation/`\n- **Examples**: See `V2/examples/` and `examples_and_demos/` for usage examples\n- **Issues**: Report bugs on [GitHub Issues](https://github.com/erfanzohrabi/spymot/issues)\n\n### Citations\nIf you use Spymot in your research, please cite the relevant database sources:\n- **ELM Database**: Kumar et al. (2022) Nucleic Acids Research\n- **PROSITE**: Sigrist et al. (2021) Nucleic Acids Research\n- **AlphaFold2**: Jumper et al. (2021) Nature\n\n---\n\n## \ud83d\udcc4 License\n\nThis project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.\n\n---\n\n## \ud83c\udfc6 Acknowledgments\n\n- **ELM Consortium** for the comprehensive linear motif database\n- **SIB Swiss Institute of Bioinformatics** for PROSITE patterns\n- **DeepMind** for AlphaFold2 structure predictions\n- **Cancer research community** for functional validation of motifs\n- **Scientific community** for advancing protein structure prediction\n\n---\n\n## \ud83d\udd17 Related Tools\n\n- **SignalP**: Professional signal peptide prediction\n- **ELM Database**: Eukaryotic Linear Motif resource\n- **Pfam**: Protein family database\n- **COSMIC**: Cancer mutation database\n- **AlphaFold Database**: 3D structure predictions\n\n---\n\n## \ud83d\udcca Repository Statistics\n\n- **Total Motifs**: 316+ curated patterns\n- **Cancer-Relevant**: 200+ oncological motifs\n- **Signal Peptides**: 100+ targeting sequences\n- **Test Coverage**: 94.6% of must-detect motifs\n- **Documentation**: 40+ pages of comprehensive guides\n- **Examples**: Multiple usage scenarios and output formats\n\n---\n\n## \ud83c\udfaf Use Cases\n\n### Cancer Biology Research\n- **Oncogene Analysis**: Detect degrons, phosphodegrons, and regulatory motifs in tumor suppressors\n- **Drug Target Identification**: Find druggable motifs and interaction sites\n- **Biomarker Discovery**: Identify cancer-relevant motifs in protein panels\n- **Pathway Analysis**: Map signaling motifs across cancer-related pathways\n\n### Protein Trafficking Studies\n- **Secretory Pathway**: Signal peptides, ER retention, Golgi targeting\n- **Organellar Import**: Mitochondrial, peroxisomal, nuclear targeting signals\n- **Membrane Trafficking**: Endocytic motifs, vesicle transport signals\n- **Subcellular Localization**: Predict protein distribution and trafficking routes\n\n### Structural Biology\n- **AlphaFold Validation**: Assess 3D structure confidence for motif regions\n- **Domain Organization**: Identify functional domains and interaction motifs\n- **Structure-Function**: Correlate motif locations with structural features\n- **Experimental Design**: Guide mutagenesis and functional studies\n\n---\n\n## \ud83d\ude80 Future Roadmap\n\n### Planned Enhancements\n- **Machine Learning Integration**: AI-powered motif prediction\n- **Multi-species Analysis**: Cross-species motif conservation\n- **Web Interface**: Browser-based analysis platform\n- **API Development**: RESTful API for integration\n- **Cloud Deployment**: Scalable cloud-based analysis\n\n### Research Directions\n- **Dynamic Motif Analysis**: Time-resolved motif detection\n- **Network Analysis**: Protein interaction network integration\n- **Drug Design**: Structure-based drug discovery tools\n- **Personalized Medicine**: Patient-specific motif analysis\n\n---\n\n**\ud83e\uddec Spymot: Empowering protein functional analysis through comprehensive motif detection and structure validation.**\n\n*Developed by Erfan Zohrabi for cancer biology research and protein functional analysis.*\n\n---\n\n## \ud83d\udce6 **Python Package Publishing**\n\n### **Build Package**\n```bash\n# Install build tools\npip install build twine\n\n# Build package\npython -m build\n\n# Check package\ntwine check dist/*\n```\n\n### **Publish to PyPI**\n```bash\n# Upload to PyPI\ntwine upload dist/*\n\n# Install from PyPI\npip install spymot\n```\n\n### **Package Information**\n- **Name**: `spymot`\n- **Version**: `2.0.0`\n- **Description**: Advanced Protein Motif Detection with AlphaFold Structural Validation\n- **Author**: Erfan Zohrabi\n- **License**: MIT\n- **Python**: >=3.8\n- **Dependencies**: numpy, requests, click, PyYAML\n\n---\n\n## \ud83d\udccb Quick Reference\n\n### Installation Commands\n```bash\n# Python Package (Recommended)\npip install spymot\n\n# Development Installation\ngit clone https://github.com/erfanzohrabi/spymot.git\ncd spymot\npip install -e .\n\n# Legacy V2 (Manual)\ncd spymot/V2\npip install -r requirements.txt\npip install -e .\n\n# Legacy V1 (Manual)\ncd spymot/V1\npip install -r requirements.txt\n```\n\n### Basic Usage Commands\n```bash\n# Python Package (Recommended)\nspymot --help\nspymot v1 analyze protein.fasta --format json\nspymot v2 analyze protein.fasta --database all --cancer-only\nspymot interactive --version v2\n\n# Legacy V2 Enhanced\npython -m spymot_enhanced.cli analyze protein.fasta --database all --format json\npython -m spymot_enhanced.cli interactive\n\n# Legacy V1 Basic\npython -m spymot.cli analyze protein.fasta --format json\npython -m spymot.cli pdb 1TUP --format json\n```\n\n### Test Commands\n```bash\n# V2 Tests\ncd V2 && python test_enhanced_system.py\n\n# V1 Tests\ncd V1 && python test_system.py\n```\n\n---\n\n*For detailed documentation, examples, and advanced usage, see the respective README files in V1/ and V2/ directories.*\n\n---\n\n## \ud83c\udf89 **What's New: Python Package Support**\n\nSpymot is now available as a **Python package**! This major update provides:\n\n\u2705 **Unified Installation**: `pip install spymot` \n\u2705 **Single Command Interface**: `spymot v1` and `spymot v2` \n\u2705 **Easy Integration**: Import directly in Python scripts \n\u2705 **Version Management**: Automatic versioning and updates \n\u2705 **Development Tools**: Complete development environment setup \n\u2705 **PyPI Ready**: Ready for distribution on Python Package Index \n\n**Upgrade your workflow:**\n```bash\n# Old way (manual)\ncd V2 && python -m spymot_enhanced.cli analyze protein.fasta\n\n# New way (package)\npip install spymot\nspymot v2 analyze protein.fasta --database all --cancer-only\n```\n\nThe Python package maintains full backward compatibility while providing a much cleaner and more professional user experience!\n",
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