EDoP distance between sets of incomplete permutations: Application to bacteria classification based on gene order

Xinrui Zhou, Amihood Amir, Concettina Guerra, Gadi Landau, Jarek Rossignac

Research output: Contribution to journalArticlepeer-review

Abstract

In this work, we extend measures of distance between permutations to support incomplete permutations. Modeling and comparing incomplete permutations are a challenging computational problem of practical importance in many applications in bioinformatics and social science. We show that the proposed distance measure admits a closed-form expression and can be efficiently computed on sets of permutations involving several missing elements. We demonstrate the proposed method on the classification of bacteria from different phyla based on gene order.

Original languageEnglish
Pages (from-to)1193-1202
Number of pages10
JournalJournal of Computational Biology
Volume25
Issue number11
DOIs
StatePublished - Nov 2018

Bibliographical note

Funding Information:
Amir, Guerra, Landau, and X. Zhao were, in part, supported by the U. S.–Israel Binational Science Foundation (BSF) grant 2014028. Amir and Landau were, in part, supported by the Israel Science Foundation 571-14.

Publisher Copyright:
© Copyright 2018, Mary Ann Liebert, Inc., publishers 2018.

Keywords

  • classification
  • distance
  • gene order
  • permutations

ASJC Scopus subject areas

  • Modeling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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