Construction of web-based Database for Haliotis SNP
Ji-Eun Jeong, Jae-Bong Lee, Se-Won Kang, Moon-Ki Baek, Yeon-Soo Han1, Tae-Jin Choi2, Jung-Ha Kang3 and Yong-Seok Lee
Department of Parasitology, College of Medicine and Frontier Inje Research for Science and Technology, Inje University, Busan, 614-735, Korea; 1Department of Agricultural Biology, Chonnam National University, Gwangju 500-757, Korea; 2Department of Microbi

The Web-based Haliotis SNP database was constructed on the basis of Intel Server Platform ZSS130 dual Xeon 3.2 GHz cpu and Linux-based (Cent OS) operating system. Haliotis related sequences (2,830 nucleotide sequences, 9,102 EST sequences) were downloaded through NCBI taxonomy browser. In order to eliminate vector sequences, we conducted vector masking step using cross match software with vector sequence database. In addition, poly-A tails were removed using Trimmest software from EMBOSS package. The processed sequences were clustered and assembled by TGICL package (TIGR tools) equipped with CAP3 software. A web-based interface (Haliotis SNP Database, was developed to enable optimal use of the clustered assemblies. The Clustering Res. menu shows the contig sequences from the clustering, the alignment results and sequences from each cluster. And also we can compare any sequences with Haliotis related sequences in BLAST menu. The search menu is equipped with its own search engine so that it is possible to search all of the information in the database using the name of a gene, accession number and/or species name. Taken together, the Web-based SNP database for Haliotis will be valuable to develop SNPs of Haliotis in the future.

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