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Bioinformatics. 2015 May 15;31(10):1553-60. doi: 10.1093/bioinformatics/btu856. Epub 2015 Jan 10.

Shifted Hamming distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping.

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Computer Science Department, Department of Electrical and Computer Engineering, Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA 15213, USA and Department of Computer Engineering, Bilkent University, Bilkent, Ankara 06800, Turkey.



Calculating the edit-distance (i.e. minimum number of insertions, deletions and substitutions) between short DNA sequences is the primary task performed by seed-and-extend based mappers, which compare billions of sequences. In practice, only sequence pairs with a small edit-distance provide useful scientific data. However, the majority of sequence pairs analyzed by seed-and-extend based mappers differ by significantly more errors than what is typically allowed. Such error-abundant sequence pairs needlessly waste resources and severely hinder the performance of read mappers. Therefore, it is crucial to develop a fast and accurate filter that can rapidly and efficiently detect error-abundant string pairs and remove them from consideration before more computationally expensive methods are used.


We present a simple and efficient algorithm, Shifted Hamming Distance (SHD), which accelerates the alignment verification procedure in read mapping, by quickly filtering out error-abundant sequence pairs using bit-parallel and SIMD-parallel operations. SHD only filters string pairs that contain more errors than a user-defined threshold, making it fully comprehensive. It also maintains high accuracy with moderate error threshold (up to 5% of the string length) while achieving a 3-fold speedup over the best previous algorithm (Gene Myers's bit-vector algorithm). SHD is compatible with all mappers that perform sequence alignment for verification.

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