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http://dx.doi.org/10.5352/JLS.2010.20.3.411

Construction of Web-Based Database for Anisakis Research  

Lee, Yong-Seok (Department of Parasitology, Inje University College of Medicine)
Baek, Moon-Ki (Department of Parasitology, Inje University College of Medicine)
Jo, Yong-Hun (Department of Agricultural Biology, College of Agriculture and Life Science, Chonnam National University)
Kang, Se-Won (Department of Parasitology, Inje University College of Medicine)
Lee, Jae-Bong (Department of Parasitology, Inje University College of Medicine)
Han, Yeon-Soo (Department of Agricultural Biology, College of Agriculture and Life Science, Chonnam National University)
Cha, Hee-Jae (Department of Parasitology, Pusan National University College of Medicine)
Yu, Hak-Sun (Department of Parasitology and Genetics, Kosin University College of medicine)
Ock, Mee-Sun (Department of Parasitology, Pusan National University College of Medicine)
Publication Information
Journal of Life Science / v.20, no.3, 2010 , pp. 411-415 More about this Journal
Abstract
Anisakis simplex is one of the parasitic nematodes, and has a complex life cycle in crustaceans, fish, squid or whale. When people eat under-processed or raw fish, it causes anisakidosis and also plays a critical role in inducing serious allergic reactions in humans. However, no web-based database on A. simplex at the level of DNA or protein has been so far reported. In this context, we constructed a web-based database for Anisakis research. To build up the web-based database for Anisakis research, we proceeded with the following measures: First, sequences of order Ascaridida were downloaded and translated into the multifasta format which was stored as database for stand-alone BLAST. Second, all of the nucleotide and EST sequences were clustered and assembled. And EST sequences were translated into amino acid sequences for Nuclear Localization Signal prediction. In addition, we added the vector, E. coli, and repeat sequences into the database to confirm a potential contamination. The web-based database gave us several advantages. Only data that agrees with the nucleotide sequences directly related with the order Ascaridida can be found and retrieved when searching BLAST. It is also very convenient to confirm contamination when making the cDNA or genomic library from Anisakis. Furthermore, BLAST results on the Anisakis sequence information can be quickly accessed. Taken together, the Web-based database on A. simplex will be valuable in developing species specific PCR markers and in studying SNP in A. simplex-related researches in the future.
Keywords
Web-based database; Anisakis; interface; sequence information;
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1 Tatusov, R., N. Fedorova, J. Jackson, A. Jacobs, B. Kiryutin, E. Koonin, D. Krylov, R. Mazumder, S. Mekhedov, A. Nikolskaya, B. S. Rao, S. Smirnov, A. Sverdlov, S. Vasudevan, Y. Wolf, J. Yin, and D. Natale. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41.   DOI   ScienceOn
2 UCSC Genome Browser. http://genome.ucsc.edu
3 Yu, H. S., S. K. Park, K. H. Lee, S. J. Lee, S. H. Choi, M. S. Ock, and H. J. Jeong. 2007. Anisakis simplex: analysis of expressed sequence tags (ESTs) of third-stage larva. Exp. Parasitol. 117, 51-56.   DOI
4 Lee, E. J., Y. C. Kim, H. G. Jeong, and O. J. Lee. 2009. The mucosal changes and influencing factors in upper gastrointestinal anisakiasis: analysis of 141 cases. Korean J. Gastroenterol 53, 90-97.
5 Nesiohelix samarangae EST database. http://edunabi.com/~nsdb
6 Lee, Y. S., S. W. Kang, Y. H. Jo, H. C. Gwak, S. H. Chae, S. H. Choi, I. Y. Ahn, H. S. Park, Y. S. Han, and W. G. Kho. 2006. Bioinformatic analysis of NLS (Nuclear Localization Signals)-containing proteins from MOLLUSKS. The Korean Journal of Malacology 22, 109-113.
7 Moneo, I., M. L. Caballero, R. Rodriguez-Perez, A. I. Rodriguez-Mahillo, and M. Gonzalez-Munoz. 2007. Sensitization to the fish parasite Anisakis simplex: clinical and laboratory aspects. Parasitol Res. 101, 1051-1055.   DOI
8 Moon, E. K., J. O. Kim, Y. H. Xuan, Y. S. Yun, S. W. Kang, Y. S. Lee, T. I. Ahn, Y. C. Hong, D. I. Chung, and H. H. Kong. 2009. Construction of EST database for comparative gene studies of acanthamoeba. Korean J. Parasitol. 47, 103-107.   DOI
9 NCBI (National Center for Biotechnology Information). http://www.ncbi.nlm.nih.gov/
10 Pampiglione, S., F. Rivasi, M. Criscuolo, A. De Benedittis, A. Gentile, S. Russo, M. Testini, and M. Villan. 2002. Human anisakiasis in Italy: a report of eleven new cases. Pathol. Res. Pract. 198, 429-434.   DOI
11 Pertea, G., X. Huang, F. Liang, V. Antonescu, R. Sultana, S. Karamycheva, Y. Lee, J. White, F. Cheung, B. Parvizi, J. Tsai, and J. Quackenbush. 2003. TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19, 651-652.   DOI
12 PlasmoDB. http://plasmodb.org
13 Rice, P., I. Longden, and A. Bleasby. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends in Genetics 16, 276-277.   DOI
14 Choi, S. J., J. C. Lee, M. J. Kim, G. Y. Hur, S. Y. Shin, and H. S. Park. 2009. The clinical characteristics of Anisakis allergy in Korea. Korean J. Intern. Med. 24, 160-163.   DOI
15 Altschul, S. F., W. Gish, W. Miller, E. W. Meyers, and D. J. Lipman. 1990. Basic local alignment search tool. Journal of Molecular Biology 215, 403-410.   DOI
16 Bouree, P., A. Paugam, and J. C. Petithory. 1995. Anisakidosis: report of 25 cases and review of the literature. Comp. Immunol. Microbiol. Infect Dis. 18, 75-84.   DOI
17 Burge, C. and S. Karlin. 1997. Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology 268, 78-94.   DOI
18 Cokol, M., R. Nair, and B. Rost. 2000. Finding nuclear localization signals. EMBO Rep. 1, 411-415.   DOI
19 Ensembl. http://www.ensembl.org
20 Genomes online Database V 3.0. http://www.genomesonline.org
21 Huang, X. and A. Madan. 1999. CAP3: A DNA sequence assembly program. Genome Res. 9, 868-877.   DOI
22 Ishikura, H. and K. Kikuchi. 1990. Intestinal anisakiasis in Japan. Infected fish, sero-immunology, diagnosis, and prevention. pp. 129-143, Springer Verlag. Tokyo
23 Ishikura, H., K. Kikuchi, K. Nagasawa, T. Ooiwa, H. Takamiya, N. Sato, and K. Sugane. 1993. Anisakidae and anisakidosis. Prog. Clin. Parasitol. 3, 43-102.