title: A computer-based method of selecting clones for a full-length cDNA project: simultaneous collection of negligibly redundant and variant cDNAs.
abstract: 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.
authors.affiliation: Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, Yokohama, 230-0045, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Osato
authors.forename: Masayoshi
authors.initials: M
authors.lastname: Itoh
authors.forename: Hideaki
authors.initials: H
authors.lastname: Konno
authors.forename: Shinji
authors.initials: S
authors.lastname: Kondo
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Shibata
authors.forename: Piero
authors.initials: P
authors.lastname: Carninci
authors.forename: Toshiyuki
authors.initials: T
authors.lastname: Shiraki
authors.forename: Akira
authors.initials: A
authors.lastname: Shinagawa
authors.forename: Takahiro
authors.initials: T
authors.lastname: Arakawa
authors.forename: Shoshi
authors.initials: S
authors.lastname: Kikuchi
authors.forename: Kouji
authors.initials: K
authors.lastname: Sato
authors.forename: Jun
authors.initials: J
authors.lastname: Kawai
authors.forename: Yoshihide
authors.initials: Y
authors.lastname: Hayashizaki
mesh_terms: 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
chemical_list: D018076:DNA, Complementary; D018744:DNA, Plant