OMH
Order Min Hash (OMH) is a locality-sensitive hashing (LSH) method designed to edit distance in sequence alignment. It improves upon the existing minHash LSH, which approximates the Jaccard similarity, by considering not only the k-mer contents of the sequences but also the relative order of the k-mers within the sequences. This refinement allows OMH to provide a more accurate estimation of the likelihood of two sequences having a proper alignment while maintaining the computational efficiency of LSH methods.
Topic
Phylogeny;Sequence assembly;Metagenomics
Detail
Operation: Editing;Sequence assembly
Software interface: Command-line interface
Language: C++,Perl,Python
License: Not stated
Cost: Free of charge
Version name: v0.0.2
Credit: The Gordon and Betty Moore Foundation, the US National Institutes of Health, The Shurl and Kay Curci Foundation, and the Schmidt Futures program.
Input: -
Output: -
Contact: Guillaume Marçais gmarcais@cs.cmu.edu ,Carl Kingsford carlk@cs.cmu.edu
Collection: -
Maturity: -
Publications
- Locality-sensitive hashing for the edit distance.
- Marçais G, et al. Locality-sensitive hashing for the edit distance. Locality-sensitive hashing for the edit distance. 2019; 35:i127-i135. doi: 10.1093/bioinformatics/btz354
- https://doi.org/10.1093/BIOINFORMATICS/BTZ354
- PMID: 31510667
- PMC: PMC6612865
Download and documentation
Source: https://github.com/Kingsford-Group/omhismb2019/releases/tag/v0.0.2
Documentation: https://github.com/Kingsford-Group/omhismb2019/blob/master/README.md
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