International Mammalian Genome Society

The 14th International Mouse Genome Conference (2000)

Table of Contents * Genes, Physical Mapping and Sequencing * Gene Identification * Bioinformatics * Common Resources * RIKEN Session * Functional Genomics * Complex Traits * Mutagenesis * Developmental Genetics and Differentiation * Verne Chapman Memorial Lecture I and II

C17. Computer-Based Methods for a Mouse Full-Length cDNA Project: Database and Real-Time Sequence Clustering for Construction of a Non-Redundant cDNA Library

Hideaki Konno, Yoshifumi Fukunishi, Kazuhiro Shibata, Masayoshi Itoh, Piero Carninci, Yuichi Sugahara and Yoshihide Hayashizaki
Laboratory for Genome Exploration Research Group, Genome Sciences Center (GSC), Genome Science Laboratory, Tsukuba Institute, CREST, Japan Sciences and Technology Corporation (JST) 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan

We developed computer-based method for constructing a non-redundant mouse full-length cDNA library. Our cDNA library construction process comprises assessment of library quality, sequencing the 3' ends inserts and clustering, and completing a re-array to generate a non-redundant library from a redundant one. After the cDNA libraries are generated, we sequence the 5' ends of the inserts to check the quality of the library, then we determine the sequencing priority of each library. Selected libraries undergo large-scale sequencing of the 3' ends of the inserts and clustering of the tag sequences. After clustering, the non-redundant library is constructed from the original libraries, which have redundant clones. All libraries, plates, clones, sequences, and clusters uniquely identified, and all information is saved in the database according to this identifier. The non-redundant library and this database are being used for farther analysis such as entire sequencing, microarray analysis and protein-protein interaction analysis.