ArticleAlgorithms for molecular biology : AMB2025
Engineering rank queries on bit vectors and strings.
Article in Algorithms for molecular biology : AMB, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Adding rank support to strings over a fixed-sized alphabet has numerous applications. Prominent among those is the (bidirectional) FM-Index which is commonly utilized to index and analyze genomic data. At its core lies the rank operation on the Burrows-Wheeler-Transform (BWT) which, given a position in the BWT and a character, answers how often the specified character appears from the start to that position. Implementing those rank queries is usually based on bit vectors with rank support. In this work, we discuss three implementation improvements. First, a novel approach named paired-blocks that reduces the space overhead of the support structure by half to a total of only
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