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. 2001 Feb;11(2):281-9.
doi: 10.1101/gr.gr-1457r.

Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library

H Konno  1 , Y Fukunishi, K Shibata, M Itoh, P Carninci, Y Sugahara, Y Hayashizaki
Affiliations

Computer-based methods for the mouse full-length cDNA encyclopedia: real-time sequence clustering for construction of a nonredundant cDNA library

H Konno et al. Genome Res. 2001 Feb.

Abstract

We developed computer-based methods for constructing a nonredundant mouse full-length cDNA library. Our cDNA library construction process comprises assessment of library quality, sequencing the 3' ends of inserts and clustering, and completing a re-array to generate a nonredundant library from a redundant one. After the cDNA libraries are generated, we sequence the 5' ends of the inserts to check the quality of the library; then we determine the sequencing priority of each library. Selected libraries undergo large-scale sequencing of the 3' ends of the inserts and clustering of the tag sequences. After clustering, the nonredundant library is constructed from the original libraries, which have redundant clones. All libraries, plates, clones, sequences, and clusters are uniquely identified, and all information is saved in the database according to this identifier. At press time, our system has been in place for the past two years; we have clustered 939,725 3' end sequences into 127,385 groups from 227 cDNA libraries/sublibraries (see http://genome.gse.riken.go.jp/).

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Figures

Figure 1
Figure 1
Number of clusters for various clustering conditions. P = 10E−20, 10E−25, and 10E−30 stand for P = 10−20, 10−25, and 10−30, respectively.
Figure 2
Figure 2
Distribution of priming sites.
Figure 3
Figure 3
Data flow and identifiers (IDs).
Figure 4
Figure 4
Plate bar code and identifier (ID) rules.
See this image and copyright information in PMC

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