On algorithmic complexity of biomolecular sequence assembly problem

Narzisi, G., Mishra, B., Schatz, M. C. (2014) On algorithmic complexity of biomolecular sequence assembly problem. In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer, pp. 183-195. ISBN 16113349 - ISSN978-331907952-3

URL: http://link.springer.com/chapter/10.1007%2F978-3-3...
DOI: 10.1007/978-3-319-07953-0_15

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. © 2014 Springer International Publishing.

Item Type: Book Section
Uncontrolled Keywords: Genome Assembly NP-complete Problem Optimality Sequence Assembly Problem
Subjects: bioinformatics
bioinformatics > computational biology
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Schatz lab
CSHL labs > Wigler lab
Depositing User: Matt Covey
Date: 2014
Date Deposited: 01 Aug 2014 16:15
Last Modified: 01 Aug 2014 16:15
URI: http://repository.cshl.edu/id/eprint/30658

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