MUMmerGPU specifications

Information


Unique identifier OMICS_02151
Name MUMmerGPU
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++
Parallelization CUDA
License Artistic License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for MUMmerGPU

MUMmerGPU in publications

 (3)
PMCID: 5555494
PMID: 28835734
DOI: 10.1177/1176934317724764

[…] in the past, many parallel algorithms, programs, and tools have been developed using cuda based on desktop gpu cards. for example, in the bioinformatics field, several cuda-based tools, such as mummergpu, cuda-meme, and cuda-blastp, have been proposed. clustalw is a well-known multiple sequence alignment tool, which is used to align a set of sequences by repeatedly (or called progressively) […]

PMCID: 3654629
PMID: 23710465
DOI: 10.1155/2013/939460

[…] on the sharing of a gpu among vms, their overheads are not negligible. , is the evaluation results of several biological applications. in this evaluation, we ran the barracuda [], cudasw++ [], mummergpu [], and cuda-meme []. the x-axis denotes the workloads and biological applications, and the y-axis is normalized execution time which includes disk i/o, cpu computation, and gpu […]

PMCID: 2222658
PMID: 18070356
DOI: 10.1186/1471-2105-8-474

[…] for analysis of these data, but researchers will need ever faster, high-throughput alignment tools running on inexpensive hardware to keep up with new sequence technologies., this paper describes mummergpu, an open-source high-throughput parallel pairwise local sequence alignment program that runs on commodity graphics processing units (gpus) in common workstations. mummergpu uses the new […]


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MUMmerGPU institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, MD, USA

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