A computer-based method of selecting clones for a full-length cDNA project: Simultaneous collection of negligibly redundant and variant cDNAs

Naoki Osato, Masayoshi Itoh, Hideaki Konno, Shinji Kondo, Kazuhiro Shibata, Piero Carninci, Toshiyuki Shiraki, Akira Shinagawa, Takahiro Arakawa, Shoshi Kikuchi, Kouji Sato, Jun Kawai, Yoshihide Hayashizaki

Research output: Contribution to journalArticlepeer-review

24 Citations (Scopus)

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 ∼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.

Original languageEnglish
Pages (from-to)1127-1134
Number of pages8
JournalGenome Research
Volume12
Issue number7
DOIs
Publication statusPublished - 2002
Externally publishedYes

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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