Better greedy sequence clustering with fast banded alignment

DOI10.4230/LIPICS.WABI.2017.3zbMATH Open1443.92136MaRDI QIDQ5111792FDOQ5111792

Authors: Brian Brubach, Jay Ghurye, Mihai Pop, Aravind Srinivasan 

Publication date: 27 May 2020

Recommendations

• A heuristic clustering method based on neighbor-seeds for 454 sequencing data
• Fast embedding methods for clustering tens of thousands of sequences
• Clustering Near-Identical Sequences for Fast Homology Search
• A Comparative Study of Protein Sequence Clustering Algorithms
• Estimating sequence similarity from read sets for clustering next-generation sequencing data

zbMATH Keywords

string algorithmsmetagenomicssequence clustering

Mathematics Subject Classification ID

Protein sequences, DNA sequences (92D20)

Cites Work

• Algorithms on Strings, Trees and Sequences
• Title not available (Why is that?)
• A faster algorithm computing string edit distances
• An \(O(ND)\) difference algorithm and its variations
• A fast bit-vector algorithm for approximate string matching based on dynamic programming

Cited In (5)

• Efficient relaxed search in hierarchically clustered sequence datasets
• Estimating sequence similarity from read sets for clustering next-generation sequencing data
• A heuristic clustering method based on neighbor-seeds for 454 sequencing data
• Fast embedding methods for clustering tens of thousands of sequences
• A succinct four Russians speedup for edit distance computation and one-against-many banded alignment

Uses Software

• PHYLIP
• ClustalW
• Clustal X
• Cd-hit
• DNACLUST

This page was built for publication: Better greedy sequence clustering with fast banded alignment

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q5111792)