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 language | English (US) |
|---|---|
| Title of host publication | Algorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings |
| Publisher | Springer Verlag |
| Pages | 183-195 |
| Number of pages | 13 |
| Volume | 8542 LNBI |
| ISBN (Print) | 9783319079523 |
| DOIs | |
| State | Published - 2014 |
| Event | 1st International Conference on Algorithms for Computational Biology, AlCoB 2014 - Tarragona, Spain Duration: Jul 1 2014 → Jul 3 2014 |
Publication series
| Name | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) |
|---|---|
| Volume | 8542 LNBI |
| ISSN (Print) | 03029743 |
| ISSN (Electronic) | 16113349 |
Other
| Other | 1st International Conference on Algorithms for Computational Biology, AlCoB 2014 |
|---|---|
| Country | Spain |
| City | Tarragona |
| Period | 7/1/14 → 7/3/14 |
Fingerprint
Keywords
- Genome Assembly
- NP-complete Problem
- Optimality
- Sequence Assembly Problem
ASJC Scopus subject areas
- Computer Science(all)
- Theoretical Computer Science
Cite this
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 proceeding › Conference contribution
}
TY - GEN
T1 - On algorithmic complexity of biomolecular sequence assembly problem
AU - Narzisi, Giuseppe
AU - Mishra, Bhubaneswar
AU - Schatz, Michael C.
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
KW - Genome Assembly
KW - NP-complete Problem
KW - Optimality
KW - Sequence Assembly Problem
UR - http://www.scopus.com/inward/record.url?scp=84904016064&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84904016064&partnerID=8YFLogxK
U2 - 10.1007/978-3-319-07953-0_15
DO - 10.1007/978-3-319-07953-0_15
M3 - Conference contribution
AN - SCOPUS:84904016064
SN - 9783319079523
VL - 8542 LNBI
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 183
EP - 195
BT - Algorithms for Computational Biology - First International Conference, AlCoB 2014, Proceedings
PB - Springer Verlag
ER -