Question

What data structure allows for memory-efficient read mapping by enabling the searching of a pattern within a reference genome without storing the entire suffix tree?

Accepted Answer

The data structure is the Burrows-Wheeler Transform combined with the FM-index. A suffix tree is a powerful tool for finding patterns in a genome, but it requires an enormous amount of memory because it stores every possible suffix of the reference sequence in a tree structure. The Burrows-Wheeler Transform solves this by rearranging the characters of a genome to group similar patterns together, which creates a highly compressible representation of the sequence. The FM-index, which stands for Full-text index in Minute space, is a compressed index built on top of this transform that allows for rapid searching of patterns without decompressing the data or storing the full suffix tree. To find a pattern, the FM-index uses the last-to-first mapping property, where the algorithm moves backward through the Burrows-Wheeler Transform to identify the range of occurrences of a query pattern within the original sequence. Because it only requires storing a small auxiliary table alongside the transformed string, it reduces the memory footprint from gigabytes to megabytes, allowing a massive human genome to be indexed on standard hardware.

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What data structure allows for memory-efficient read mapping by enabling the searching of a pattern within a reference genome without storing the entire suffix tree?