[Construction and application of bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer].
As a key component of life science, bioinformatics has been widely applied in genomics, transcriptomics, and proteomics. However, the requirement of high-performance computers rather than common personal computers for constructing a bioinformatics platform significantly limited the application of bioinformatics in aquatic science. In this study, we constructed a bioinformatic analysis platform for aquatic pathogen based on the MilkyWay-2 supercomputer. The platform consisted of three functional modules, including genomic and transcriptomic sequencing data analysis, protein structure prediction, and molecular dynamics simulations. To validate the practicability of the platform, we performed bioinformatic analysis on aquatic pathogenic organisms. For example, genes of Flavobacterium johnsoniae M168 were identified and annotated via Blast searches, GO and InterPro annotations. Protein structural models for five small segments of grass carp reovirus HZ-08 were constructed by homology modeling. Molecular dynamics simulations were performed on out membrane protein A of Aeromonas hydrophila, and the changes of system temperature, total energy, root mean square deviation and conformation of the loops during equilibration were also observed. These results showed that the bioinformatic analysis platform for aquatic pathogen has been successfully built on the MilkyWay-2 supercomputer. This study will provide insights into the construction of bioinformatic analysis platform for other subjects.
Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
Xiang
X
Fang
Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
Ning-qiu
N
Li
Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
Xiao-zhe
XZ
Fu
Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
Kai-bin
KB
Li
Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
Qiang
Q
Lin
Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
Li-hui
LH
Liu
Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
Cun-bin
CB
Shi
Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province,Key Laboratory of Fishery Drug Development of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China.
Shu-qin
SQ
Wu
D016980:Aeromonas hydrophila / Q000737:chemistry; D000818:Animals; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry; D002347:Carps / Q000821:virology; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D005417:Flavobacterium / Q000235:genetics; D056004:Molecular Dynamics Simulation; D012087:Reoviridae / Q000235:genetics; D014764:Viral Proteins / Q000737:chemistry
D001425:Bacterial Outer Membrane Proteins; D014764:Viral Proteins