High-throughput sequence alignment using Graphics Processing Units

@article{Schatz2007HighthroughputSA,
  title={High-throughput sequence alignment using Graphics Processing Units},
  author={Michael C. Schatz and Cole Trapnell and Arthur L. Delcher and Amitabh Varshney},
  journal={BMC Bioinformatics},
  year={2007},
  volume={8},
  pages={474 - 474}
}
BackgroundThe recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated for several purposes, including genotyping, genome resequencing, metagenomics, and de novo genome assembly projects. Sequence alignment programs such as MUMmer have proven essential for analysis of these data, but researchers will need ever faster, high-throughput alignment tools… Expand
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References

SHOWING 1-10 OF 39 REFERENCES
Bio-sequence database scanning on a GPU
TLDR
A new approach to bio-sequence database scanning using computer graphics hardware to gain high performance at low cost and reformulated the Smith-Waterman dynamic programming algorithm in terms of computer graphics primitives. Expand
Fast algorithms for large-scale genome alignment and comparison.
TLDR
A suffix-tree algorithm that can align the entire genome sequences of eukaryotic and prokaryotic organisms with minimal use of computer time and memory is described and a method to align more distantly related genomes by detecting protein sequence homology is described. Expand
Initial Experiences Porting a Bioinformatics Application to a Graphics Processor
TLDR
This work focuses on porting to the GPU the most time-consuming loop, which accounts for nearly 50% of the total execution time, and shows preliminary results show that the loop code achieves a speedup of 3x while the whole application with a single loop optimization, achieves aspeedup of 1.2x. Expand
Improved tools for biological sequence comparison.
  • W. Pearson, D. Lipman
  • Biology, Medicine
  • Proceedings of the National Academy of Sciences of the United States of America
  • 1988
TLDR
Three computer programs for comparisons of protein and DNA sequences can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. Expand
Comparative genome assembly
TLDR
A novel algorithm for comparative genome assembly that can accurately assemble a typical bacterial genome in less than four minutes on a standard desktop computer is described. Expand
Efficient multiple genome alignment
TLDR
New algorithms and a software tool 'Multiple Genome Aligner' (MGA for short) that efficiently computes multiple genome alignments of large, closely related DNA sequences. Expand
LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA.
TLDR
Both LAGAN and Multi-LAGAN compare favorably with other leading alignment methods in correctly aligning protein-coding exons, especially between distant homologs such as human and chicken, or human and fugu. Expand
Alignment of whole genomes.
TLDR
Using an efficient data structure called a suffix tree, the system is able to rapidly align sequences containing millions of nucleotides and should facilitate analysis of syntenic chromosomal regions, strain-to-strain comparisons, evolutionary comparisons and genomic duplications. Expand
Basic local alignment search tool.
A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP)Expand
A Memory Model for Scientific Algorithms on Graphics Processors
TLDR
A memory model is presented to analyze and improve the performance of scientific algorithms on graphics processing units (GPUs) and incorporates many characteristics of GPU architectures including smaller cache sizes, 2D block representations, and the 3C's model to analyze the cache misses. Expand
...
1
2
3
4
...