A new distributed alignment-free approach to compare whole proteomes

DOI10.1016/J.TCS.2017.06.017zbMATH Open1380.68470OpenAlexW2726669970MaRDI QIDQ1676313FDOQ1676313

Authors Concettina Guerra, Cinzia Pizzi, Umberto Ferraro-Petrillo

Publication date 6 November 2017

Published in Theoretical Computer Science (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.tcs.2017.06.017

zbMATH Keywords

bioinformaticsdistributed systemsalignment-free distancesmismatchesaverage common substring

Mathematics Subject Classification ID

Problems related to evolution (92D15) Protein sequences, DNA sequences (92D20) Algorithms on strings (68W32)

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Cites work

• Algorithms in bioinformatics. 15th international workshop, WABI 2015, Atlanta, GA, USA, September 10--12, 2015. Proceedings
• Longest common substring with approximately \(k\) mismatches
• Longest common substrings with \(k\) mismatches
• Sequence similarity measures based on bounded Hamming distance
• \(k\)-difference matching in amortized linear time for all the words in a text

Cited in

(2)

• Analysis of proteomics data: block \(k\)-mean alignment
• SimDiv: A New Solution for Protein Comparison

Describes a project that uses

Uses Software

• PHYLIP
• Hadoop
• ALFRED
• CloudPhylo
• CVTree3
• FASTdoop
• SparkSW
• Spark

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