Automated cDNA Information System
for Large Scale cDNA Project
Hideaki Konno 12

hkonno@rtc.riken.go.jp

Yuichi Sugahara 1

sugahara@rtc.riken.go.jp

Kazuhiro Shibata

1

shibata@rtc.riken.go.jp

Yoshifumi Fukunishi 12

fukunisi@rtc.riken.go.jp

Yoshihide Hayashizaki 1
yosihide@rtc.riken.go.jp

1 Laboratory for Exploration Research Project, Genomic Sciences Center(GSC) andGenome Science Lab, RIKEN Life Science Tsukuba Center, the Institute of Physicaland Chemical Research (RIKEN) 3-1-1 Koyadai, Tsukuba, Ibaraki 305, Japan
2 CREST, Japan Science and Technology Corporation (JST)1 Introduction
We have been making e ort to collect various Mouse cDNA clones as large scale Mouse cDNA project.
It is aiming at collecting all kind of expressed full length Mouse cDNA clones. The rst phase of thisproject is to collect non-redundant cataloged cDNA clone bank. It is necessary for sequence data
analysis and further applications of cDNA clones.
Comparing two full length cDNA clones, if the end part of sequences are di erent, these clones areobviously di erent clones. If the end part of sequence is equivalent, these clones may be equivalentclone practically. It is obviously far easier to compare both end tip of tagged sequences than tocompare whole sequences, especially in case of the sequence is long. And it may be very rare case thatdi erent clones with same 5'-end and 3'-end sequences.
It is e ective way to classify cDNA clones, sequencing 5'-end and 3'-end and comparing previously
sequenced data. We have developed automated cDNA classi cation system to make non-redundant
cDNA clone collection.

2 System and Method
The clustering is done by several steps. All of these steps are automated.
After 5'-end and 3'-end parts are sequenced, they are stored into database entry with its cDNA
library informations. We are using SYBASE System XI RDBMS for managing sequence and librarydata. At the rst step, vector and primer sequence are removed from each sequenced data. NeedlemanWunsch algorithm [1] based method was applied to nd the edge of primer sequences.
And then, picked out 100b sequences from each end of sequences as sequence tag. Non complex
repeated sequences like poly-A are excluded before making the tags. Then, the tags are made into ahomology search with in-house 3'-end or 5'-end databases using BLAST [2] and FASTA [3]. We haveexamined this homology search conditions by computer simulation and actual data analysis.
If it is not found any equivalent sequence, then new group is created and added to in-house
database. Otherwise the tag is added as new member of the existing group. And then, created newgroup tag is made into homology search with known sequence database and EST database. The
homolologous entry's information, i.e GID, ACCESSION, DEFINITION, etc. and homology scores
are stored as the homology search results. The data sets of known sequence data and EST data weretaken from NCBI ftp server [4]. We use nt { All Non-redundant GenBank+EMBL+DDBJ+PDB
sequence (but no EST, STS, GSS, or HTGS sequences) { as known sequence data, and est human andest mouse as EST database.
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These analyses are done automatically and each results are stored into the database.
And we made easy to retrieve the cDNA information from the database, using WWW browsers (i.e.
Netscape Navigator). We are using apache httpd with CGI program and Java applet for retrieving
cDNA informations. CGI programs are mainly written in perl and C language. This server has notbeen opened to public, because it is part of our laboratory information system. Sequenced cDNA
clone information will be opened near future.

Acknowledgements
This study has been supported by Special Coordination Funds and a Research Grant for the Genome
Exploration Research Project from the Science and Technology Agency of the Japanese Government,
CREST (Core Research for Evolutional Science and Technology) of Japan Science and Technology
Corporation (JST), and a Grant-in-Aid for Scienti c Research on Priority Areas and Human Genome
Program from the Ministry of Education and Culture, Japan to Y.H.

References[1] Needleman, S.B., Wunsch, C.D., A general method applicable to the search for similarities in theamino acid sequence of two proteins, J. Mol. Biol., 48(3):443{53, 1970.
[2] Altschul, S.F., Gish, W., Miller, W., Myers, E.W., and Lipman, D.J., Basic local alignment searchtool, J. Mol. Biol., 215:403{10, 1990.
[3] Pearson, W.R. and Lipman, D.J., Improved tools for biological sequence analysis, Pro. Natl.
Acad. Sci., 85:2444{2448, 1988.
[4] ftp://ncbi.nlm.nih.gov/blast/db/.

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