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» Multiple Sequence Alignment Using Reconfigurable Computing
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121
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BMCBI
2007
233views more  BMCBI 2007»
15 years 2 months ago
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
Background: To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching s...
Isaac T. S. Li, Warren Shum, Kevin Truong
RECOMB
1998
Springer
15 years 6 months ago
A polyhedral approach to RNA sequence structure alignment
Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U. It is a generally single-stranded molecule where the bases form hydrogen bonds within the same m...
Hans-Peter Lenhof, Knut Reinert, Martin Vingron
129
Voted
BIBE
2005
IEEE
126views Bioinformatics» more  BIBE 2005»
15 years 7 months ago
Highly Scalable and Accurate Seeds for Subsequence Alignment
We propose a method for finding seeds for the local alignment of two nucleotide sequences. Our method uses randomized algorithms to find approximate seeds. We present a dynamic ...
Abhijit Pol, Tamer Kahveci
133
Voted
ICCV
2005
IEEE
16 years 4 months ago
Periodic Motion Detection and Segmentation via Approximate Sequence Alignment
A method for detecting and segmenting periodic motion is presented. We exploit periodicity as a cue and detect periodic motion in complex scenes where common methods for motion se...
Ivan Laptev, Josh Wills, Patrick Pérez, Ser...
ICCS
2005
Springer
15 years 7 months ago
SWAT: A New Spliced Alignment Tool Tailored for Handling More Sequencing Errors
Abstract. There are several computer programs that align mRNA with its genomic counterpart to determine exon boundaries. Though most of these programs perform such alignment effici...
Yifeng Li, Hesham H. Ali