Crate genomic_system_finder_core 

genomic-system-finder-core

Core library for Genomic System Finder — detection of macromolecular systems (secretion systems, CRISPR-Cas, pili, etc.) in protein sequences.

Overview

Genomic System Finder searches protein sequences against HMM profiles, clusters nearby hits, and evaluates candidate systems based on gene composition models. It supports:

• Ordered replicons: assembled genomes with known gene order
• Unordered sequences: draft/fragmented genomes
• Gembase format: multi-replicon databases

Architecture

• config: Configuration and scoring parameters
• model: System model definitions (mandatory, accessory, forbidden genes)
• profile: HMM profile management and search
• sequence: FASTA parsing and replicon handling
• hit: HMM search hit representation
• cluster: Gene clustering algorithms
• system: System detection, scoring, and selection
• report: Output generation (TSV, JSON)

Re-exports

pub use config::Config;

pub use config::ConfigBuilder;

pub use config::DbType;

pub use config::RepliconTopology;

pub use error::MacsyError;

pub use system::GenomicSystemFinder;

Modules

cluster

Gene clustering algorithms.

config

Configuration for Genomic System Finder.

error

hit

HMM search hit representation.

model

System model definitions.

profile

HMM profile management and search.

report

Output generation for Genomic System Finder results.

sequence

FASTA sequence parsing and replicon representation.

system

System detection, scoring, and best solution selection.