Genome Research

Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
QUICK SEARCH:   [advanced]


     

Published online before print January 18, 2001, 10.1101/gr.GR-1457R
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow All Versions of this Article:
GR-1457Rv1
11/2/281    most recent
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Konno, H.
Right arrow Articles by Hayashizaki, Y.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Konno, H.
Right arrow Articles by Hayashizaki, Y.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us   Add to Digg   Add to Reddit   Add to Technorati  
What's this?

Vol. 11, Issue 2, 281-289, February 2001

METHODS
Computer-Based Methods for the Mouse Full-Length cDNA Encyclopedia: Real-Time Sequence Clustering for Construction of a Nonredundant cDNA Library

Hideaki Konno,1,3 Yoshifumi Fukunishi,2,3 Kazuhiro Shibata,2 Masayoshi Itoh,2 Piero Carninci,2 Yuichi Sugahara,2 and Yoshihide Hayashizaki1,2,3

1 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama 230-0045, Japan; 2 Genome Science Laboratory, RIKEN Tsukuba Institute, Tsukuba 305-0074, Japan; 3 Core Research for Evolutional Science and Technology, of Japan Science and Technology Corporation, Tsukuba 305-0074, Japan

We developed computer-based methods for constructing a nonredundant mouse full-length cDNA library. Our cDNA library construction process comprises assessment of library quality, sequencing the 3' ends of inserts and clustering, and completing a re-array to generate a nonredundant 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 nonredundant library is constructed from the original libraries, which have redundant clones. All libraries, plates, clones, sequences, and clusters are uniquely identified, and all information is saved in the database according to this identifier. At press time, our system has been in place for the past two years; we have clustered 939,725 3' end sequences into 127,385 groups from 227 cDNA libraries/sublibraries (see http://genome.gse.riken.go.jp/).

[The sequence data described in this paper have been submitted to the DDBJ data library under accession nos. AV00011-AV175734, AV204013-AV382295, and BB561685-BB609425.]

3 Corresponding author.

11:281-289 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg   Add to Reddit Reddit   Add to Technorati Technorati    What's this?


This article has been cited by other articles:


Home page
 J. Exp. Biol.Home page
A. Y. Gracey
Interpreting physiological responses to environmental change through gene expression profiling
J. Exp. Biol., May 1, 2007; 210(9): 1584 - 1592.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. Masoudi-Nejad, K. Tonomura, S. Kawashima, Y. Moriya, M. Suzuki, M. Itoh, M. Kanehisa, T. Endo, and S. Goto
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments.
Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W459 - W462.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
K. W. Choy, C. C. Wang, A. Ogura, T. K. Lau, M. S. Rogers, K. Ikeo, T. Gojobori, D. S. C. Lam, and C. P. Pang
Genomic annotation of 15,809 ESTs identified from pooled early gestation human eyes
Physiol Genomics, March 13, 2006; 25(1): 9 - 15.
[Abstract] [Full Text] [PDF]

Home page
 Plant Cell PhysiolHome page
T. Nanjo, N. Futamura, M. Nishiguchi, T. Igasaki, K. Shinozaki, and K. Shinohara
Characterization of Full-length Enriched Expressed Sequence Tags of Stress-treated Poplar Leaves
Plant Cell Physiol., December 15, 2004; 45(12): 1738 - 1748.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
T. Nishiyama, T. Fujita, T. Shin-I, M. Seki, H. Nishide, I. Uchiyama, A. Kamiya, P. Carninci, Y. Hayashizaki, K. Shinozaki, et al.
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: Implication for land plant evolution
PNAS, June 24, 2003; 100(13): 8007 - 8012.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
P. Carninci, K. Waki, T. Shiraki, H. Konno, K. Shibata, M. Itoh, K. Aizawa, T. Arakawa, Y. Ishii, D. Sasaki, et al.
Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia
Genome Res., June 1, 2003; 13(6): 1273 - 1289.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
M. Zavolan, S. Kondo, C. Schonbach, J. Adachi, D. A. Hume, RIKEN GER Group, GSL Members, Y. Hayashizaki, and T. Gaasterland
Impact of Alternative Initiation, Splicing, and Termination on the Diversity of the mRNA Transcripts Encoded by the Mouse Transcriptome
Genome Res., June 1, 2003; 13(6): 1290 - 1300.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
N. Osato, M. Itoh, H. Konno, S. Kondo, K. Shibata, P. Carninci, T. Shiraki, A. Shinagawa, T. Arakawa, S. Kikuchi, et al.
A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs
Genome Res., July 1, 2002; 12(7): 1127 - 1134.
[Abstract] [Full Text] [PDF]


Home Help [Feedback] [For Subscribers] [Archive] [Search] [Contents]
Genes Dev. Learn. Mem.
Protein Science RNA Genome Res.