TY  - JOUR
A1  - Osato, Naoki
A1  - Itoh, Masayoshi
A1  - Konno, Hideaki
A1  - Kondo, Shinji
A1  - Shibata, Kazuhiro
A1  - Carninci, Piero
A1  - Shiraki, Toshiyuki
A1  - Shinagawa, Akira
A1  - Arakawa, Takahiro
A1  - Kikuchi, Shoshi
A1  - Sato, Kouji
A1  - Kawai, Jun
A1  - Hayashizaki, Yoshihide
T1  - A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs
Y1  - 2002/07/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1127 
EP  - 1134 
DO  - 10.1101/gr.75202 
VL  - 12 
IS  - 7 
UR  - http://genome.cshlp.org/content/12/7/1127.abstract 
N2  - We describe a computer-based method that selects representative clones for full-length sequencing in a full-length cDNA project. Our method classifies end sequences using two kinds of criteria, grouping, and clustering. Grouping places together variant cDNAs, family genes, and cDNAs with sequencing errors. Clustering separates those cDNA clones into distinct clusters. The full-length sequences of the clones selected by grouping are determined preferentially, and then the sequences selected by clustering are determined. Grouping reduced the number of rice cDNA clones for full-length sequencing to 21% and mouse cDNA clones to 25%. Rice full-length sequences selected by grouping showed a 1.07-fold redundancy. Mouse full-length sequences showed a 1.04-fold redundancy, which can be reduced by ∼30% from the selection using our previous method. To estimate the coverage of unique genes, we used FANTOM (Functional Annotation of RIKEN Mouse cDNA Clones) clusters (the RIKEN Genome Exploration Research Group 2001). Grouping covered almost all unique genes (93% of FANTOM clusters), and clustering covered all genes. Therefore, our method is useful for the selection of appropriate representative clones for full-length sequencing, thereby greatly reducing the cost, labor, and time necessary for this process.[The programs used in this paper are available online at http://genome.gsc.riken.go.jp/software/2C.] 
ER  -