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Multiple samples alignment for GC-MS data in parallel on Sector/Sphere
YANG Huihua REN Hongjun LI Lingqiao DUAN Lixin GUO Tuo DU Lingling QI Xiaoquan
Journal of Computer Applications
2013, 33 (01):
215-218.
DOI: 10.3724/SP.J.1087.2013.00215
To deal with the problem that the process of Gas Chromatography-Mass Spectrography (GC-MS) data is complex and time consuming which delays the whole experimental progress, taking the alignment of multiple samples as an example, a parallel framework for processing GC-MS data on Sector/Sphere was proposed, and an algorithm of aligning multiple samples in parallel was implemented. First, the similarity matrix of all the samples was computed, then the sample set was divided into small sample sets according to hierarchical clustering and samples in each set were aligned respectively, finally the results of each set were merged according to the average sample of the set. The experimental results show that the error rate of the parallel alignment algorithm is 2.9% and the speedup ratio reaches 3.29 using the cluster with 4 PC, which can speed up the process at a high accuracy, and handle the problem that the processing time is too long.
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