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Motivation Although there are many different algorithms and software tools for aligning sequencing reads, fast gapped sequence search is far from solved. Strong interest in fast alignment is best reflected in the $106 prize for the Innocentive competition on aligning a collection of reads to a given database of reference genomes. In addition, de novo assembly of next-generation sequencing long reads...
Fast alignment of small sequences to a very large sequence has recently been under attention of many researchers, due to the applications in processing the biological sequences and specially mapping the short reads of Next Generation Sequencing to an already assembled reference genome. The MEMOCODE 2012 contest was aimed to design a very efficient exact DNA sequence matching method to map a huge number...
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