13 releases (8 breaking)
0.9.1 | Sep 2, 2024 |
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0.8.0 | Jun 28, 2024 |
0.6.0 | Dec 13, 2023 |
0.5.1 | Aug 31, 2023 |
0.3.0 | Jun 25, 2023 |
#13 in Biology
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🎼🧬 lightmotif
A lightweight platform-accelerated library for biological motif scanning using position weight matrices.
🗺️ Overview
Motif scanning with position weight matrices (also known as position-specific scoring matrices) is a robust method for identifying motifs of fixed length inside a biological sequence. They can be used to identify transcription factor binding sites in DNA, or protease cleavage site in polypeptides. Position weight matrices are often viewed as sequence logos:
The lightmotif
library provides a Rust crate to run very efficient
searches for a motif encoded in a position weight matrix. The position
scanning combines several techniques to allow high-throughput processing
of sequences:
- Compile-time definition of alphabets and matrix dimensions.
- Sequence symbol encoding for fast table look-ups, as implemented in HMMER[1] or MEME[2]
- Striped sequence matrices to process several positions in parallel, inspired by Michael Farrar[3].
- Vectorized matrix row look-up using
permute
instructions of AVX2.
Other crates from the ecosystem provide additional features if needed:
lightmotif-io
is a crate with parser implementations for various count matrix, frequency matrix and position-specific scoring matrix formats such as TRANSFAC or JASPAR.lightmotif-tfmpvalue
is an exact reimplementation of the TFM-PVALUE[4] algorithm for converting between a score and a p-value for a given scoring matrix.
This is the Rust version, there is a Python package available as well.
💡 Example
use lightmotif::*;
use lightmotif::abc::Nucleotide;
// Create a count matrix from an iterable of motif sequences
let counts = CountMatrix::<Dna>::from_sequences(
["GTTGACCTTATCAAC", "GTTGATCCAGTCAAC"]
.into_iter()
.map(|s| EncodedSequence::encode(s).unwrap()),
)
.unwrap();
// Create a PSSM with 0.1 pseudocounts and uniform background frequencies.
let pssm = counts.to_freq(0.1).to_scoring(None);
// Use the pipeline to encode the target sequence into a striped matrix
let seq = "ATGTCCCAACAACGATACCCCGAGCCCATCGCCGTCATCGGCTCGGCATGCAGATTCCCAGGCG";
let encoded = EncodedSequence::encode(seq).unwrap();
let mut striped = encoded.to_striped();
// Organize layout of striped matrix to allow scoring with PSSM.
striped.configure(&pssm);
// Compute scores for every position of the matrix.
let scores = pssm.score(&striped);
// Scores can be extracted into a Vec<f32>, or indexed directly.
let v = scores.unstripe();
assert_eq!(scores[0], -23.07094);
assert_eq!(v[0], -23.07094);
// Find the highest scoring position.
let best = scores.argmax().unwrap();
assert_eq!(best, 18);
// Find the positions above an absolute score threshold.
let indices = scores.threshold(10.0);
assert_eq!(indices, []);
This example uses a dynamic dispatch pipeline, which selects the best available backend (AVX2, SSE2, NEON, or a generic implementation) depending on the local platform.
⏱️ Benchmarks
Both benchmarks use the MX000001
motif from PRODORIC[5], and the
complete genome of an
Escherichia coli K12 strain.
Benchmarks were run on a i7-10710U CPU running @1.10GHz, compiled with --target-cpu=native
.
-
Score every position of the genome with the motif weight matrix:
test bench_avx2 ... bench: 4,510,794 ns/iter (+/- 9,570) = 1029 MB/s test bench_sse2 ... bench: 26,773,537 ns/iter (+/- 57,891) = 173 MB/s test bench_generic ... bench: 317,731,004 ns/iter (+/- 2,567,370) = 14 MB/s
-
Find the highest-scoring position for a motif in a 10kb sequence (compared to the PSSM algorithm implemented in
bio::pattern_matching::pssm
):test bench_avx2 ... bench: 12,797 ns/iter (+/- 380) = 781 MB/s test bench_sse2 ... bench: 62,597 ns/iter (+/- 43) = 159 MB/s test bench_generic ... bench: 671,900 ns/iter (+/- 1,150) = 14 MB/s test bench_bio ... bench: 1,193,911 ns/iter (+/- 2,519) = 8 MB/s
💭 Feedback
⚠️ Issue Tracker
Found a bug ? Have an enhancement request ? Head over to the GitHub issue tracker if you need to report or ask something. If you are filing in on a bug, please include as much information as you can about the issue, and try to recreate the same bug in a simple, easily reproducible situation.
📋 Changelog
This project adheres to Semantic Versioning and provides a changelog in the Keep a Changelog format.
⚖️ License
This library is provided under the open-source MIT license.
This project was developed by Martin Larralde during his PhD project at the European Molecular Biology Laboratory in the Zeller team.
📚 References
- Eddy, Sean R. ‘Accelerated Profile HMM Searches’. PLOS Computational Biology 7, no. 10 (20 October 2011): e1002195. doi:10.1371/journal.pcbi.1002195.
- Grant, Charles E., Timothy L. Bailey, and William Stafford Noble. ‘FIMO: Scanning for Occurrences of a given Motif’. Bioinformatics 27, no. 7 (1 April 2011): 1017–18. doi:10.1093/bioinformatics/btr064.
- Farrar, Michael. ‘Striped Smith–Waterman Speeds Database Searches Six Times over Other SIMD Implementations’. Bioinformatics 23, no. 2 (15 January 2007): 156–61. doi:10.1093/bioinformatics/btl582.
- Touzet, Hélène, and Jean-Stéphane Varré. ‘Efficient and Accurate P-Value Computation for Position Weight Matrices’. Algorithms for Molecular Biology 2, no. 1 (2007): 1–12. doi:10.1186/1748-7188-2-15.
- Dudek, Christian-Alexander, and Dieter Jahn. ‘PRODORIC: State-of-the-Art Database of Prokaryotic Gene Regulation’. Nucleic Acids Research 50, no. D1 (7 January 2022): D295–302. doi:10.1093/nar/gkab1110.