E2FM: an encrypted and compressed full-text index for collections of genomic sequences

Bioinformatics
Ferdinando MontecuolloRoberto Tagliaferri

Abstract

Next Generation Sequencing (NGS) platforms and, more generally, high-throughput technologies are giving rise to an exponential growth in the size of nucleotide sequence databases. Moreover, many emerging applications of nucleotide datasets-as those related to personalized medicine-require the compliance with regulations about the storage and processing of sensitive data. We have designed and carefully engineered E 2 FM -index, a new full-text index in minute space which was optimized for compressing and encrypting nucleotide sequence collections in FASTA format and for performing fast pattern-search queries. E 2 FM -index allows to build self-indexes which occupy till to 1/20 of the storage required by the input FASTA file, thus permitting to save about 95% of storage when indexing collections of highly similar sequences; moreover, it can exactly search the built indexes for patterns in times ranging from few milliseconds to a few hundreds milliseconds, depending on pattern length. Source code is available at https://github.com/montecuollo/E2FM . ferdinando.montecuollo@unicampania.it. Supplementary data are available at Bioinformatics online.

References

Mar 6, 2009·Genome Biology·Ben LangmeadSteven L Salzberg
Sep 23, 2010·Human Molecular Genetics·Julienne M MullaneyScott E Devine
Oct 13, 2011·Algorithms for Molecular Biology : AMB·Vladimir Yanovsky
May 7, 2016·Bioinformatics·Kana ShimizuGunnar Rätsch
Aug 4, 2016·Bioinformatics·Subrata Saha, Sanguthevar Rajasekaran

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