Bioinformatics Study On Expressed Sequence Tags From Fenneropenaeus Chinensis

Bioinformatics methods are used to analyze and manage expressed sequence tags (ESTs) which are generated by large-scale sequencing of a cDNA library from cephalothorax of a wild, female, adult Chinese shrimp (Fenneropenaeus chinensis). The 10446 ESTss have been assembled into 1399 contigs and 1421 singletons. BLAST and Interproscan are localized in a PC-CLUSTER to annotate the ESTss. A web-based BLAST is also constructed to facilitate the process. And the contigs and ESTs sequences are formatted as subject database. By similarity search, about 442 ESTss were found possibly encoding immune related proteins, such as lysozyme, lectin, serine protease, serpin, thioredoxin, SOD and so on. After careful studying their relative importance to immune response and the possibility of the match, seventeen sequences of interest were selected for further experiment, including ESTss analogous to 11.5KD antibacterial peptide, lysozyme, serine protease and its inhibitor, lectin, antifreeze protein, et al. Primers designed according to the sequences were used to amplify the corresponding ESTss from both blood and cephalothorax cDNA library. The amplified sequences are sequenced and compared with their template. Seven of them are expected sequences.To efficiently use the ESTs data, a relationship database is constructed to store and organize them. The database management system (DBMS) is MS SQL Server from Microsoft. Raw sequence files and alignment results are normalized to tables acceptable to the DBMS. The database could be visited by both MS SQL Server and web. Webpages based on ASP are written to connect and visit the database.