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Next Generation Sequencing (NGS) platforms and, more generally,high-throughput technologies are giving rise to an exponential growth in thesize of nucleotide sequence databases. Moreover, many emerging applications ofnucleotide datasets -- as those related to personalized medicine -- require thecompliance with regulations about the storage and processing of sensitive data.We have designed and carefully engineered E2FM-index, a new full-text index inminute space which was optimized for compressing and encrypting nucleotidesequence collections in FASTA format and for performing fast pattern-searchqueries. E2FM-index allows to build self-indexes which occupy till to 1/20 ofthe storage required by the input FASTA file, thus permitting to save about 95%of storage when indexing collections of highly similar sequences; moreover, itcan exactly search the built indexes for patterns in times ranging from fewmilliseconds to a few hundreds milliseconds, depending on pattern length.Supplementary material and supporting datasets are available throughBioinformatics Online and https://figshare.com/s/6246ee9c1bd730a8bf6e.

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