plasann 1.1.6

PlasAnn - Plasmid sequence annotation tool with enhanced dependency management

PlasAnn - Plasmid Annotation Tool

This tool is designed for annotating plasmid sequences from FASTA or GenBank files. It provides comprehensive annotation including coding sequences (CDS), origins of replication (oriC/oriV), origins of transfer (oriT), transposons, replicons, and non-coding RNAs.

Features

• Automatic Database Download: Databases are downloaded automatically on first run
• Flexible Input: Single files or entire folders of FASTA/GenBank files
• Gene Prediction: Uses Prodigal for accurate gene calling
• Mobile Element Detection: Identifies transposons, insertion sequences, and origins
• Visualizations: Generates circular plasmid maps
• Batch Processing: Process multiple files simultaneously
• Enhanced Annotation: Optional UniProt BLAST for comprehensive protein annotation

Installation

Dependencies

This tool requires the following external programs:

• BLAST+ (makeblastdb, blastn, blastx, blastp)
• Prodigal (CDS prediction)
• Infernal (cmscan, cmpress - for ncRNA detection)

Install PlasAnn

pip install plasann

Installing External Dependencies

For macOS (Apple Silicon M1/M2):

brew tap brewsci/bio
brew install blast prodigal infernal

For Linux (Ubuntu/Debian):

sudo apt install ncbi-blast+ prodigal infernal

For other systems: Install from source following the official documentation for BLAST+, Prodigal, and Infernal.

Verify Installation

PlasAnn --check-deps

Usage

Basic Commands

PlasAnn -i <input_file_or_directory> -o <output_directory> -t <file_type>

Parameters

• -i, --input: Path to input file or directory containing FASTA or GenBank files
• -o, --output: Path to output directory where results will be stored
• -t, --type: Type of input files: fasta, genbank, or auto

Examples

Single FASTA file:

PlasAnn -i plasmid.fasta -o results -t fasta

Folder of FASTA files:

PlasAnn -i fasta_folder/ -o results -t fasta

GenBank file (retain existing annotations):

PlasAnn -i plasmid.gb -o results -t genbank --retain

GenBank file (re-annotate with Prodigal):

PlasAnn -i plasmid.gb -o results -t genbank --overwrite

Auto-detect mixed file types:

PlasAnn -i mixed_folder/ -o results -t auto

Enhanced annotation with UniProt:

PlasAnn -i plasmid.fasta -o results -t fasta --uniprot-blast

GenBank Processing Options

When using GenBank files, you can choose:

• --retain: Use existing CDS annotations in the GenBank file (default)
• --overwrite: Ignore existing annotations and re-predict genes using Prodigal

Additional Options

• --uniprot-blast: Run enhanced UniProt BLAST annotation (slower but more comprehensive)
• --min-identity: Minimum identity percentage for UniProt BLAST hits (default: 50%)
• --version: Show version information
• --check-deps: Check external dependency status

Output Files

For each input file, PlasAnn generates:

• CSV Table: Detailed annotation table with gene information
• GenBank File: Annotated GenBank file with all features
• Plasmid Map: Circular visualization of the annotated plasmid (PNG format)
• Enhanced CSV: Additional file with UniProt annotations (if --uniprot-blast used)

Troubleshooting

Check dependencies:

PlasAnn --check-deps

Common issues:

• Ensure BLAST+, Prodigal, and Infernal are properly installed
• Check that input files are valid FASTA or GenBank format
• For very short sequences (<100bp), CDS prediction may not work well

Contact

For questions or issues, contact: [e-mail]

Citation

If you use PlasAnn in your research, please cite:

PlasAnn: Comprehensive Plasmid Annotation Pipeline
Habibul Islam
University of Rochester