Parameterized complexity of asynchronous border minimization

Robert Ganian, Martin Kronegger, Andreas Pfandler, Alexandru Popa

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Microarrays are research tools used in gene discovery as well as disease and cancer diagnostics. Two prominent but challenging problems related to microarrays are the Border Minimization Problem (BMP) and the Border Minimization Problem with given placement (P-BMP). In this paper we investigate the parameterized complexity of natural variants of BMP and P-BMP, termed BMPe and P-BMPe respectively, under several natural parameters. We show that BMPe and P-BMPe are in FPT under the following two combinations of parameters: (1) the size of the alphabet (c), the maximum length of a sequence (string) in the input (ℓ) and the number of rows of the microarray (r); and, (2) the size of the alphabet and the size of the border length (o). Furthermore, P-BMPe is in FPT when parameterized by c and ℓ. We complement our tractability results with corresponding hardness results.

Original languageEnglish
Title of host publicationTheory and Applications of Models of Computation - 12th Annual Conference, TAMC 2015, Proceedings
EditorsRahul Jain, Sanjay Jain, Frank Stephan
PublisherSpringer Verlag
Pages428-440
Number of pages13
ISBN (Electronic)9783319171418
DOIs
Publication statusPublished - 2015
Event12th Annual Conference on Theory and Applications of Models of Computation, TAMC 2015 - Singapore, Singapore
Duration: May 18 2015May 20 2015

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9076
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Other

Other12th Annual Conference on Theory and Applications of Models of Computation, TAMC 2015
CountrySingapore
CitySingapore
Period5/18/155/20/15

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science(all)

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