RT Journal
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
JF Genome Research 
JO Genome Research 
YR 2002 
FD July 01 
VO 12 
IS 7 
SP 1127 
OP 1134 
DO 10.1101/gr.75202 
UL http://genome.cshlp.org/content/12/7/1127.abstract 
AB 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.]