String data structures | Substring indices

FM-index

In computer science, an FM-index is a compressed full-text substring index based on the Burrows–Wheeler transform, with some similarities to the suffix array. It was created by Paolo Ferragina and Giovanni Manzini, who describe it as an opportunistic data structure as it allows compression of the input text while still permitting fast substring queries. The name stands for Full-text index in Minute space. It can be used to efficiently find the number of occurrences of a pattern within the compressed text, as well as locate the position of each occurrence. The query time, as well as the required storage space, has a sublinear complexity with respect to the size of the input data. The original authors have devised improvements to their original approach and dubbed it "FM-Index version 2". A further improvement, the alphabet-friendly FM-index, combines the use of compression boosting and wavelet trees to significantly reduce the space usage for large alphabets. The FM-index has found use in, among other places, bioinformatics. (Wikipedia).

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Related pages

DSPACE | Time complexity | Compressed suffix array | Burrows–Wheeler transform | Substring index | Wavelet Tree | Suffix array | Sequence alignment