A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs.
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 approximately 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 (). 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.
Osato
Naoki
N
Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan.
Itoh
Masayoshi
M
Konno
Hideaki
H
Kondo
Shinji
S
Shibata
Kazuhiro
K
Carninci
Piero
P
Shiraki
Toshiyuki
T
Shinagawa
Akira
A
Arakawa
Takahiro
T
Kikuchi
Shoshi
S
Sato
Kouji
K
Kawai
Jun
J
Hayashizaki
Yoshihide
Y
D000818:Animals; D001483:Base Sequence; D003001:Cloning, Molecular / Q000379:methods*; D018076:DNA, Complementary / Q000145:classification / Q000235:genetics*; D018744:DNA, Plant / Q000145:classification / Q000235:genetics; D015723:Gene Library; D005796:Genes / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D012275:Oryza / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods*; D012815:Signal Processing, Computer-Assisted
D018076:DNA, Complementary; D018744:DNA, Plant