Crate genomic_system_finder_hmm 

genomic-system-finder-hmm

A pure Rust implementation of HMMER3-compatible profile HMM search.

This crate provides a WASM-compatible alternative to HMMER’s hmmsearch, implementing the Plan7 Viterbi algorithm for scoring protein sequences against profile HMMs in HMMER3/b format.

Features

• Parse HMMER3/b format HMM profile files
• Viterbi algorithm for Plan7 HMMs with local entry/exit
• Multi-domain detection
• E-value computation using Gumbel extreme value distribution
• No external dependencies (pure Rust, WASM-compatible)

Usage

use genomic_system_finder_hmm::{parser, pipeline, SearchOptions, TargetSequence};

let hmms = parser::parse_hmm_file(Path::new("profile.hmm")).unwrap();
let targets = vec![TargetSequence {
    id: "seq1".to_string(),
    sequence: b"MKFLILACLAV...".to_vec(),
}];
let results = pipeline::hmmsearch(&hmms[0], &targets, &SearchOptions::default());

Re-exports

pub use hmm::Plan7Hmm;

pub use pipeline::DomainHit;

pub use pipeline::SearchOptions;

pub use pipeline::SearchResult;

pub use pipeline::TargetSequence;

Modules

alphabet

Amino acid alphabet encoding compatible with HMMER3.

hmm

Plan7 profile HMM data structures.

msv

MSV (Multiple Segment Viterbi) pre-filter for rapid sequence screening.

parser

Parser for HMMER3/b format HMM profile files.

pipeline

Search pipeline: orchestrates HMM search against protein sequences.

stats

Statistical calculations for E-value and P-value computation.

viterbi

Viterbi algorithm for Plan7 profile HMMs.

Enums

HmmError

Errors from HMM operations.