Comparison of Sequences of cDNA Clones Obtained from Oligo-capping cDNA Libraries with Those from UniGene

We compared in detail the characteristics of the sequences of the cDNA clones obtained by the oligo-capping method (oligo-capping clones) with that of the sequences in the UniGene database. To compare the completeness of the sequences, three new variables, “fullness-proportion of clones ” (the ratio of complete clones to total clones in a library), “fullness-proportion of genes ” (the ratio of complete genes to total genes in a library), and “fullness-proportion of database ” (the ratio of complete genes to total genes in a database sampled from a library), were defined. The fullness-proportion of clones of oligo-capping clones was 57.3%, 2.2 times larger than that of UniGene (25.9%). The fullness-proportion of genes of oligo-capping clones was 41.8%, 2.4 times larger than that of UniGene (17.8%). When gene length was restricted to ≥ 1.5 kb, the fullness-proportion of genes of oligo-capping clones was four times larger than that of UniGene. The fullness-proportion of database of oligo-capping clones was approximately the same as that of UniGene. By simulating the clone redundancy, this coincidence was found to be due to the large redundancy of the UniGene database. Consequently, the cDNA sequence database of oligo-capping clones enabled high throughput selection of full-length cDNA clones. Key words: database; full-length cDNA; UniGene; ESTs; oligo-capping 1