Construction and Application of Mouse Full-length cDNA Database

Our group has been making effort to collect mouse full-length cDNA clones as large scale Mouse cDNA project. It is aiming at collecting all kind of expressed full-length Mouse cDNA clones. The first phase of the project is to make cataloged non-redundant cDNA clone bank. It is necessary for analysis of sequence data and further applications of cDNA clones. We sequence 3’-end part of all cDNA clones and we use them as identification sequence tags. And then we classify them in terms of cluster analysis. Each cDNA cluster consists of the identical sequences. The clustering by sequence identity is achieved by an all-against-all homology search. The parameters for the homology search were optimized to give the suitable sensitivity comparing to our sequence accuracy based on the actual sequence data. If the sequence tag was new for us, it will be searched through known sequence database and EST database. We had developed automated system of series of the analysis. We improved this clustering system in accuracy and processing speed. And results of these analyses are stored into the database which is managed by RDBMS. We have gotten seventy several thousands of identical cDNA clusters of over 460,000 clones. These cDNA clones and their information are provided for further analysis. Information retrieval system for the database is available through web browser and/or UNIX command line. For example, we have applied our cDNA clones to cDNA microarray. It is very useful for further analysis to link from each spot of cDNA microarray data to each clone data.