Affiliations: Helix Research Institute, Chiba, Japan | Institute of Medical Science, University of Tokyo,
Tokyo, Japan | Present address: Biosystems Research Department,
Central Research Laboratory, Hitachi, Ltd. 1-280 Higashi-Koigakubo,
Kokubunji-shi, Tokyo, 185-8601, Japan | Present address: Kyowa Hakko Kogyo Co., Ltd., Tokyo
Research Laboratories 3-6-6 Asahi-machi, Machida-shi, Tokyo, 194-8533,
Japan
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Note: [] *
Abstract: We have developed an efficient sequence-analysis system and a
database system for clones obtained from full-length enriched cDNA libraries
made by using the oligo-capping method. We developed a
semi-automatic analysis system for 5'- and 3'-end sequences. It
pre-processes raw sequences (vector cut and accurate-sequence region
extraction), clusters the sequences, searches for similarities through public
databases, annotates completeness of clones and analyzes the ORFs in the
sequences. Newly developed or improved programs are used in each
step. A new program, ESTiMateFull is used to evaluate and to predict the
sequence-fullness based on comparisons with mRNA and EST sequences,
respectively. The ATGpr program is used to predict sequence-fullness
based on statistical information. The combination of full-length
enriched cDNA clones and ATGpr fullness prediction resulted in 70% accuracy in
the specificity and the sensitivity of the fullness predictions. For
the ORFs predicted by the ATGpr, the signal peptides are predicted and a motif
search is performed by our new system. We also developed a program
that assembles our sequences with dbEST sequences and developed a system to
retrieve clones by the characteristics of the ORFs. As keywords,
combination of various results of the analyses can be used for
retrieval. And various results such as ORF features and database
search results can be shown on the same screen by multiple
displays. Full-length clones having interesting functions can thus
be retrieved efficiently by using this system.
