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Updated: Mar 2, 2026

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA
Published on: May 9, 2011
E2FM: an encrypted and compressed full-text index for collections of genomic sequences
Ferdinando Montecuollo1, Giovannni Schmid2, Roberto Tagliaferri3
1Centro Reti, Sistemi e Servizi Informatici/CRESSI, Università degli Studi della Campania "Luigi Vanvitelli," Napoli 80133, Italy.
Motivation:
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.
Results:
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.
Availability And Implementation:
Source code is available at https://github.com/montecuollo/E2FM .
Contact:
ferdinando.montecuollo@unicampania.it.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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