A method to verify originality of sequences secretly on distributed computing environment

Kurata, K.; Nakamura, Hiroshi; Breton, Vincent

doi:10.1109/hpcasia.2004.1324051

Cited by 3 publications

(3 citation statements)

References 7 publications

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“…The program that inserts artificial mutation and splicing sites into target sequences (AMS) was written in C++ [18] The data flow of our method is shown in Figure 5. Firstly, the Escherichia coli genome was fetched from a genome database.…”

Section: Methodsmentioning

confidence: 99%

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Grid as a bioinformatic tool

et al. 2004

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doi:10.1016/j.parco.2004.07.013 www.elsevier.com/locate/parco 1094 N. Jacq et al. / Parallel Computing 30 (2004) 1093–1107 The grid is a promising tool to resolve the crucial issue of software and data integration in biology. In this paper, we have reported on our experience in the deployment of bioinformatic grid applications within the framework of the DataGrid project. These applications inquired the potential impact of grids for CPU demanding algorithms and bioinformatics web portal

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Section: Methodsmentioning

confidence: 99%

“…We inquired into a new method of verification of the originality of gene sequences secretly on public networks. Firstly, exact sequences are processed to prevent them from being reconstructed [18]. Next, this method hashes all the genomic sequences [16].…”

Section: Introductionmentioning

confidence: 99%

Grid as a bioinformatic tool

et al. 2004

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“…The experimental result on a world-wide grid environment was reported in our previous work [1]. Furthermore, we have proposed a method called Artificial Mutation and Splicing (AMS) site insertion to prevent the reconstruction of the exact sequences [6]. In this method, by means of inserting n sites of artificial mutation and splicing (AMS) into the exact sequences, the number of combinations of the reconstruction is multiplied by 2 n .…”

Section: Our Previous Studymentioning

confidence: 99%

Secret sequence comparison on public grid computing resources

Kurata

Nakamura

Breton

2005

CCGrid 2005. IEEE International Symposium on Cluster Computing and the Grid, 2005.

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Secret sequence comparison in distributed computing environments by interval sampling

Kurata¹,

Breton²,

Nakamura³

IGARSS 2004. 2004 IEEE International Geoscience and Remote Sensing (IEEE Cat. No.04CH37612)

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Once a new gene has been seunenced. it must be alreadv been resorted. and to estimate the similaritv to known verified whether or not it issimilar to previously sequenced genes. In many cases, the organization that sequenced a potentially novel gene needs to keep the sequence itself in confidence. However, to compare the potentially novel sequence with known sequences, it must either he sent as a qnery to public databases, or these databases must be downloaded onto a local computer. In both cases, the potentially new sequence is exposed to the public In this work, we propose a new method, ealled Interval Sampling, to compare sequences without leaking exact information about the new sequence. Io order to keep the exact sequence information secmt, this method samples intervals (subsequences) from a sequence, and these intervals are hashed. The hashed data are open to the public to verify the novelty of the sequence. We fmd that this method works well in parallel in a distributed computing environment, such as the Grid. The experimental results for 19797 hsapiens genes and 25ooo m.musculus genes show that the parallel implementation of this method performs reasonably well in t e m of speed and memory usage.

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A method to verify originality of sequences secretly on distributed computing environment

Cited by 3 publications

References 7 publications

Grid as a bioinformatic tool

Grid as a bioinformatic tool

Secret sequence comparison on public grid computing resources

Secret sequence comparison in distributed computing environments by interval sampling

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