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

Nucleic Acids Research
Michaël VyvermanPeter Dawyndt

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.

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Citations

Sep 27, 2012·Journal of Natural Products·Marc SlatteryJohn M Rimoldi
Jan 26, 2013·Bioinformatics·Michaël VyvermanPeter Dawyndt
Jan 11, 2013·BMC Bioinformatics·Nicolas MailletPierre Peterlongo
Nov 21, 2013·Algorithms for Molecular Biology : AMB·Sebastian Deorowicz, Szymon Grabowski
Dec 18, 2013·Bioinformatics·Francisco Fernandes, Ana T Freitas
Mar 7, 2014·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Matteo Comin, Montse Farreras
Jan 15, 2014·Briefings in Bioinformatics·Anish Man Singh ShresthaPaul Horton
Feb 5, 2014·Nucleic Acids Research·Martin C Frith, Laurent Noé
Dec 19, 2013·Briefings in Bioinformatics·Raffaele GiancarloFilippo Utro
May 27, 2015·Nucleic Acids Research·Min-Te ChouJui-Hung Hung
May 15, 2015·BMC Bioinformatics·Michaël VyvermanPeter Dawyndt
Feb 25, 2015·Frontiers in Bioengineering and Biotechnology·Travis Gagie, Simon J Puglisi
Apr 30, 2016·BioData Mining·Franco MilicchioMattia Prosperi
Oct 8, 2014·PloS One·Agnieszka DanekSzymon Grabowski
Oct 3, 2017·Bioinformatics·Haoyu ChengYun Xu
Dec 28, 2016·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Qingfeng ChenChengqi Zhang
May 22, 2019·BioMed Research International·Maleeha NajamAsad Waqar Malik

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Methods Mentioned

BETA
RNA-seq
suffix array construction

Software Mentioned

DC3
Bowtie
STELLAR
SeqAn
GPFAs
SSA
BLAST
bzip2
MUMmer
Affix

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