Using video-oriented instructions to speed up sequence comparison

By Andrzej Wozniak. 1997

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Citations in the corpus

Accelerated Profile HMM Searches (2011, methodology): “Several vector methods have been described for accelerating classical Smith/Waterman local sequence alignment [34,35], and methods for accelerating Smith/Waterman dynamic programming (DP) recursions are readily adapted to profile HMMs.”
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors (2000, methodology): “This fact has been utilized in earlier SIMD implementations (Hughey, 1996; Wozniak, 1997).”
SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications (2012, methodology): “Furthermore we obtained additional alignment information compared to SWPS3 without slowing down the original algorithm: (1) we record the optimal alignment ending positions during the SIMD SW calculation and generate the detailed alignment by a reversed SIMD SW and a banded SW.”
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation (2011, methodology): “(A) Vectors along the anti-diagonal, described by Wozniak et al [8].”
SHRiMP: Accurate Mapping of Short Color-space Reads (2009, methodology): “The SHRiMP algorithm draws upon three recent developments in the field of sequence alignment: q-gram filter approaches, introduced by Rasmussen et al [14]; spaced seeds, introduced by Califano and Rigoutsos [15] and popularized by the PatterHunter family of tools [7,10]; and specialized vector compu”
Striped Smith-Waterman speeds database searches six times over other SIMD implementations (2007, methodology): “Both the Wozniak (1997) and Rognes et al .”