On algorithmic complexity of biomolecular sequence assembly problem

Giuseppe Narzisi, Bhubaneswar Mishra, Michael C. Schatz

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

Abstract

Because of its connection to the well-known NP-complete shortest superstring combinatorial optimization problem, the Sequence Assembly Problem (SAP) has been formulated in simple and sometimes unrealistic string and graph-theoretic frameworks. This paper revisits this problem by re-examining the relationship between the most common formulations of the SAP and their computational tractability under different theoretical frameworks. For each formulation we show examples of logically-consistent candidate solutions which are nevertheless unfeasible in the context of the underlying biological problem. This material is hoped to be valuable to theoreticians as they develop new formulations of SAP as well as of guidance to developers of new pipelines and algorithms for sequence assembly and variant detection.

Original languageEnglish (US)
Title of host publicationAlgorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings
PublisherSpringer Verlag
Pages183-195
Number of pages13
Volume8542 LNBI
ISBN (Print)9783319079523
DOIs
StatePublished - 2014
Event1st International Conference on Algorithms for Computational Biology, AlCoB 2014 - Tarragona, Spain
Duration: Jul 1 2014Jul 3 2014

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume8542 LNBI
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other1st International Conference on Algorithms for Computational Biology, AlCoB 2014
CountrySpain
CityTarragona
Period7/1/147/3/14

Fingerprint

Algorithmic Complexity
Formulation
Combinatorial optimization
Superstring
Tractability
Combinatorial Optimization Problem
Pipelines
Guidance
NP-complete problem
Strings
Graph in graph theory

Keywords

  • Genome Assembly
  • NP-complete Problem
  • Optimality
  • Sequence Assembly Problem

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

Cite this

Narzisi, G., Mishra, B., & Schatz, M. C. (2014). On algorithmic complexity of biomolecular sequence assembly problem. In Algorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings (Vol. 8542 LNBI, pp. 183-195). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8542 LNBI). Springer Verlag. https://doi.org/10.1007/978-3-319-07953-0_15

On algorithmic complexity of biomolecular sequence assembly problem. / Narzisi, Giuseppe; Mishra, Bhubaneswar; Schatz, Michael C.

Algorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings. Vol. 8542 LNBI Springer Verlag, 2014. p. 183-195 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 8542 LNBI).

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

Narzisi, G, Mishra, B & Schatz, MC 2014, On algorithmic complexity of biomolecular sequence assembly problem. in Algorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings. vol. 8542 LNBI, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 8542 LNBI, Springer Verlag, pp. 183-195, 1st International Conference on Algorithms for Computational Biology, AlCoB 2014, Tarragona, Spain, 7/1/14. https://doi.org/10.1007/978-3-319-07953-0_15
Narzisi G, Mishra B, Schatz MC. On algorithmic complexity of biomolecular sequence assembly problem. In Algorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings. Vol. 8542 LNBI. Springer Verlag. 2014. p. 183-195. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)). https://doi.org/10.1007/978-3-319-07953-0_15
Narzisi, Giuseppe ; Mishra, Bhubaneswar ; Schatz, Michael C. / On algorithmic complexity of biomolecular sequence assembly problem. Algorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings. Vol. 8542 LNBI Springer Verlag, 2014. pp. 183-195 (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)).
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