Construction Of Swine Immunomics Information Platform

Immunomics is a subject researching the whole set of molecules and their targets associated with immunology, including immunogenomics, immunoproteomics and immunoinformatics. Immunoinformatics mainly consider about the aspects of immunobiology and immunology as well as clinical immunology, which takes database construction, computational statistics, mathematical modeling and computer simulation as its basic approaches. The techniques used in the database construction including data collection, database creation and administration, and they construct the baisis of immunoinformatics. The mass data gained from immunological experiment should be stored efficiently so that it can fully serve the following study.As with the accomplishment of whole pig genome sequencing and the developing of immunomic, all datas was obtained from experiments restored in various biological databases, which enriched the data in the bioinfomatics website. If there is a thematic database which integrates all the internet data associated with pig immunity, then it will be much convenient to do the research on pig immunity. Keeping this in mind, here we construct a information platform about the immunoinformatics of pig, which also contain some main bioinfomatics analysis tools, hoping to serve as a research platform for researchers.The information platform was built in the Linux+Apache+MySQL+PHP development environment. By integrating the data from PDB and IEDB, we construct all the 14 database, mainly include antibody molecular structure and sequence database, antibody light chain and heavy chain CDR sequence database, MHC molecular structure and sequence database, B cell epitope database and T cell epitope database. All these database totally contain 1787 antibody structures,6518 antibody sequences,920 light chain CDR1 sequences,750 light chain CDR2 sequences,837 light chain CDR3 sequences,873 heavy chain CDR1 sequences,912 heavy chain CDR2 sequences,909 heavy chain CDR3 sequences,833 MHC molecular structures,2988 MHC molecular sequences,1825 B cell epitope information,1804 B cell epitope sequences,1697 T cell epitope information,1437 T cell epitope sequences. The platform can perform four functions as well, including BLAST, MODELLER homologous modeling, B cell epitope prediction, and B or T cell epitope information inquiry. In the last part, we demonstrated the test using five examples to verify the each function of the platform. Among the test, the sequence of the variable region of porcine immunoglobulin kappa was used to evaluate the BLAST and MODELLER function; then we evaluated the MHC sequence BLAST and MODELLER function by sequence alignment and homologous modeling using SLA-1 molecule from Chinese Hebao pig; next we used PCV â…¡ capsid protein to test the linear B cell epitope predict function; we also used PCV â…¡ capsid protein to do the test of ID inquiry function; and finally, we searched the PCV â…¡ related T cell epitope to test the function of searching by pathogene name which the epitope come from.This project aimed to provide a directed and noninterference research tool by integrating swine immunity related information and constructing the information platform. We believed that it would be more complete since the accumulating of immunity data, and be used more extensively.