Fast spaced seed hashing

DOI10.4230/LIPICS.WABI.2017.7zbMATH Open1443.92138OpenAlexW2750157246MaRDI QIDQ5111797FDOQ5111797

Authors: Samuele Girotto, Matteo Comin, Cinzia Pizzi 

Publication date: 27 May 2020

Full work available at URL: https://dblp.uni-trier.de/db/conf/wabi/wabi2017.html#GirottoCP17

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zbMATH Keywords

spaced seeds\(k\)-mersefficient hashing

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20) Computational methods for problems pertaining to biology (92-08)

Cites Work

• Metagenomic reads binning with spaced seeds
• Irredundant tandem motifs
• On spaced seeds for similarity search
• On the complexity of the spaced seeds
• Alignment-free sequence comparison with spaced k-mers.

Cited In (3)

• Fast gapped \(k\)-mer counting with subdivided multi-way bucketed cuckoo hash tables
• Analysis of min-hashing for variant tolerant DNA read mapping
• A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets

Uses Software

• SHRiMP
• PatternHunter
• MetaProb
• SpEED
• CLARK

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