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Prospects and limitations of full-text index structures in genome analysis

Michaël Vyverman UGent, Bernard De Baets UGent, Veerle Fack UGent and Peter Dawyndt UGent (2012) NUCLEIC ACIDS RESEARCH. 40(15). p.6993-7015
abstract
The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
SHORT READ ALIGNMENT, COMPRESSED SUFFIX ARRAYS, EXTERNAL MEMORY, TREE CONSTRUCTION, FM-INDEX, EFFICIENT CONSTRUCTION, SEQUENCE COLLECTIONS, PRACTICAL ALGORITHM, INVERTED FILES, MASSIVE DATA
journal title
NUCLEIC ACIDS RESEARCH
Nucleic Acids Res.
volume
40
issue
15
pages
6993 - 7015
Web of Science type
Article
Web of Science id
000308958600008
JCR category
BIOCHEMISTRY & MOLECULAR BIOLOGY
JCR impact factor
8.278 (2012)
JCR rank
27/288 (2012)
JCR quartile
1 (2012)
ISSN
0305-1048
DOI
10.1093/nar/gks408
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
2974977
handle
http://hdl.handle.net/1854/LU-2974977
date created
2012-08-27 09:53:48
date last changed
2013-07-15 11:50:12
@article{2974977,
  abstract     = {The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared.},
  author       = {Vyverman, Micha{\"e}l and De Baets, Bernard and Fack, Veerle and Dawyndt, Peter},
  issn         = {0305-1048},
  journal      = {NUCLEIC ACIDS RESEARCH},
  keyword      = {SHORT READ ALIGNMENT,COMPRESSED SUFFIX ARRAYS,EXTERNAL MEMORY,TREE CONSTRUCTION,FM-INDEX,EFFICIENT CONSTRUCTION,SEQUENCE COLLECTIONS,PRACTICAL ALGORITHM,INVERTED FILES,MASSIVE DATA},
  language     = {eng},
  number       = {15},
  pages        = {6993--7015},
  title        = {Prospects and limitations of full-text index structures in genome analysis},
  url          = {http://dx.doi.org/10.1093/nar/gks408},
  volume       = {40},
  year         = {2012},
}

Chicago
Vyverman, Michaël, Bernard De Baets, Veerle Fack, and Peter Dawyndt. 2012. “Prospects and Limitations of Full-text Index Structures in Genome Analysis.” Nucleic Acids Research 40 (15): 6993–7015.
APA
Vyverman, M., De Baets, B., Fack, V., & Dawyndt, P. (2012). Prospects and limitations of full-text index structures in genome analysis. NUCLEIC ACIDS RESEARCH, 40(15), 6993–7015.
Vancouver
1.
Vyverman M, De Baets B, Fack V, Dawyndt P. Prospects and limitations of full-text index structures in genome analysis. NUCLEIC ACIDS RESEARCH. 2012;40(15):6993–7015.
MLA
Vyverman, Michaël, Bernard De Baets, Veerle Fack, et al. “Prospects and Limitations of Full-text Index Structures in Genome Analysis.” NUCLEIC ACIDS RESEARCH 40.15 (2012): 6993–7015. Print.