consite 0.1.0a4

ConSite: conserved-domain alignment and conserved-site visualization from protein FASTA

ConSite

ConSite is a bioinformatics tool that takes a protein FASTA sequence as input, identifies conserved domains via local Pfam/HMMER searches, detects conserved sites within aligned regions, and outputs both structured data and publication-quality visualizations.

Features

• FASTA input → conserved domain search using local Pfam database and HMMER
• Automatic domain alignment using Pfam SEED alignments
• Per-position conservation scoring (entropy, Jensen–Shannon divergence, consensus frequency)
• Conserved site detection with adjustable thresholds
• Publication-quality visualization:
  • Linear domain maps with highlighted conserved sites
  • Per-domain alignment panels with legible sequence display
  • Hollow red circles marking conserved positions
• Command-line interface (CLI) with comprehensive logging
• Reproducible outputs (JSON, TSV, PNG, Stockholm alignments)

Installation

Prerequisites

• Python 3.10 or higher
• HMMER 3.x installed and available in PATH
• Pfam database files (see Quick Start below)

Installing HMMER

macOS (Homebrew):

brew install hmmer

Linux (APT):

sudo apt-get update
sudo apt-get install hmmer

Windows (conda):

conda install -c conda-forge hmmer

Verify installation:

hmmsearch --version

From Source (1)

git clone https://github.com/yangli-evo/ConSite.git
cd ConSite

Quick Start

Option 1: Automatic Setup (Recommended) (2)

We provide helper scripts to automate the setup process:

# Make scripts executable
chmod +x scripts/*.sh

# Download and set up Pfam database
./scripts/get_pfam.sh

# Run the demo
./scripts/quickstart.sh

Note: The scripts have different purposes:

• get_pfam.sh: Downloads and prepares the Pfam database files
• quickstart.sh: Sets up the Python environment and runs the demo

Option 2: Manual Setup (2)

If you prefer to set up things manually or already have some components:

1. Install ConSite

python -m venv .venv
source .venv/bin/activate  # On Windows: .venv\Scripts\activate
pip install -e .

2. Download Pfam Database

# Create directory for Pfam files
mkdir -p pfam_db

# Download Pfam-A HMM library
curl -L -o pfam_db/Pfam-A.hmm.gz https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz
gunzip pfam_db/Pfam-A.hmm.gz

# Download Pfam-A SEED alignments
curl -L -o pfam_db/Pfam-A.seed.gz https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.seed.gz
gunzip pfam_db/Pfam-A.seed.gz

# Press the HMM library for HMMER
hmmpress pfam_db/Pfam-A.hmm

3. Run ConSite

# Basic run with example protein
consite \
  --fasta examples/P05362.fasta \
  --pfam-hmm pfam_db/Pfam-A.hmm \
  --pfam-seed pfam_db/Pfam-A.seed \
  --out results \
  --id P05362

# With custom parameters
consite \
  --fasta myprotein.fasta \
  --pfam-hmm pfam_db/Pfam-A.hmm \
  --pfam-seed pfam_db/Pfam-A.seed \
  --out results \
  --topn 5 \
  --cpu 8 \
  --jsd-top-percent 15 \
  --log results/run.log

Output Files (4)

Each run produces a results folder containing:

• query.fasta - Input sequence used for analysis
• hits.json - Structured domain hit information
• scores.tsv - Per-position conservation scores and flags (columns: pos, in_domain, jsd, entropy, is_conserved)
• domain_map.png - Full sequence domain visualization with conserved sites marked
• *_panel.png - Individual domain alignment panels showing sequence and conserved positions
• *_aligned.sto - Stockholm format alignments of query to domain HMMs
• hmmsearch.domtblout - Raw HMMER domain table output
• run.log - Complete log of all external tool executions

Command Line Options (5)

Option	Description	Default
--fasta	Input protein FASTA file	Required
--pfam-hmm	Path to Pfam-A.hmm (pressed)	Required
--pfam-seed	Path to Pfam-A.seed	Required
--out	Output directory	Required
--id	Custom run ID (default: FASTA header)	Auto-detected
--topn	Number of top domains to analyze	2
--cpu	Number of CPU cores for HMMER	4
--jsd-top-percent	Top % of positions called conserved	10.0
--log	Log file for external tool output	results/<id>/run.log
--quiet	Suppress console output	False
--keep	Preserve existing output folder	False

How It Works (6)

1. Domain Detection: Uses hmmsearch against Pfam-A.hmm to identify conserved domains
2. SEED Extraction: Pulls the corresponding Pfam SEED alignment for each hit
3. HMM Building: Creates a per-family HMM from the SEED using hmmbuild
4. Sequence Alignment: Aligns the query protein to the domain HMM using hmmalign
5. Conservation Scoring: Computes JSD and entropy scores for each position
6. Visualization: Generates domain maps and alignment panels

Current Status

What works:

• Complete domain detection and alignment pipeline
• Publication-quality visualizations
• Structured data outputs (JSON, TSV)
• Robust HMMER integration with logging

Known limitations:

• Conservation scoring currently uses query-only alignment (JSD/entropy are placeholders)
• Remote CDD mode is not yet implemented
• Conservation thresholds are relative (top X%) rather than absolute

Next steps planned:

• Integrate Pfam SEED sequences for real conservation scoring
• Add absolute conservation thresholds
• Implement remote CDD mode

Example Output (7)

For the included ICAM1 example (P05362), ConSite identifies:

• PF03921 (positions 25-115): Ig-like domain
• PF21146 (positions 219-308): Ig-like domain

The tool produces clean visualizations showing domain boundaries and conserved sites as hollow red circles.

Expected Results

After running the demo, you should see:

• A results/P05362/ folder containing all outputs
• Two domain panels: 1_PF03921_panel.png and 2_PF21146_panel.png
• A full sequence map: domain_map.png
• Structured data: hits.json and scores.tsv

Troubleshooting (8)

Common Issues

"command not found: hmmsearch"

• Install HMMER using the instructions in Prerequisites above
• Ensure it's in your PATH: which hmmsearch

"No such file or directory: pfam_db/Pfam-A.hmm"

• Run the helper script: ./scripts/get_pfam.sh
• Or manually download Pfam files as shown in Manual Setup

"Permission denied" when running scripts

• Make scripts executable: chmod +x scripts/*.sh

Large log files

• Use --quiet to suppress verbose output
• Check --log path is writable

Development (9)

Current Project Structure

ConSite/
├── src/consite/          # Main package source
│   ├── cli.py            # Command-line interface
│   ├── hmmer_local.py    # HMMER tool wrappers
│   ├── parse_domtbl.py   # HMMER output parsing
│   ├── pfam.py           # Pfam SEED extraction
│   ├── msa_io.py         # Multiple sequence alignment I/O
│   ├── conserve.py       # Conservation scoring algorithms
│   ├── viz.py            # Visualization functions
│   └── utils.py          # Shared utilities
├── examples/              # Example input files
├── scripts/               # Helper automation scripts
├── pfam_db/              # Pfam database files (not included in repo)
└── results/               # Output directory (not included in repo)

Important Notes for Collaborators

• Large files are excluded: The pfam_db/ and results/ directories are in .gitignore
• Pfam database: You'll need to download this using the helper scripts
• Virtual environment: The .venv/ folder is also excluded - you'll create your own
• Example data: The examples/P05362.fasta file is included for testing

Dependencies

• biopython ≥ 1.81 - Sequence and alignment handling
• numpy ≥ 2.0 - Numerical computations
• matplotlib ≥ 3.7 - Visualization generation
• pandas ≥ 2.0 - Data manipulation
• scipy ≥ 1.16 - Scientific computing
• Python ≥ 3.10 - Required Python version

Citation (10)

If you use ConSite in your research, please cite:

Joey Wagner, Yang Li. ConSite: conserved-domain alignment and conserved-site visualization from protein FASTA.

License

This project is licensed under the terms specified in the LICENSE file.