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Table 1 Status of DGCr1 and DGCr2 clones

From: A Drosophilafull-length cDNA resource

  DGCr1 DGCr2 Total
Clones in each release 5,849 5,061 10,910
Clones stopped while in progress* 148 739 887
   Incorrect clone 0 40 40
   Co-ligated inserts 13 493 506
   No poly(A) 9 97 106
   Transposable element (TE) 11 71 82
   Incomplete coding sequence 115 38 153
Candidate clones to be sequenced 5,701 4,322 10,023
Submitted to GenBank 5,291 3,479 8,770
Clones in progress 410 843 1,253
  1. *Quality-control analysis was carried out on clones during the sequencing process. Initial quality-control analysis was carried out for DGCr1 clones before full-length sequencing and for DGCr2 clones during the initial shotgun phase. This difference accounts for the different frequencies of error types observed in the DGCr1 and DGCr2. For example, the DGCr1 3' ESTs were generated before adding the clones to the sequencing pipeline allowing us to eliminate co-ligated clones and clones without poly(A) tails. Conversely, the DGCr2 has fewer clones with incomplete coding sequences because the DGCr2 clones were selected by aligning ESTs to the annotated genomic sequence, providing a more reliable way of selecting clones with complete ORFs than the inter se clustering of ESTs used to select the DGCr1. Clones were removed from finishing if they: were the incorrect clone as revealed by their 5'-end sequence; consisted of two cDNA molecules ligated into the same plasmid vector, as indicated by their 5'- and 3'-end reads aligning more than 300 kb apart in the genome; did not contain a poly(A) tract at their 3' end; corresponded to a member of the transposable element data set [20]; or did not extend to the ATG start site of the corresponding predicted protein in the Release 2 CDS data set. Each clone submitted to GenBank has a contiguous sequence with a phrap estimated error rate of not more than one error per 50,000 bases. Additionally, each individual base has a phred [32,33] quality score of 25 or higher. An exception to these rules was made for 475 clones from the DCGr1 clone set that were submitted to GenBank before we increased our error rate standard from one in 10,000 to one in 50,000. These clones are undergoing additional sequencing to improve their quality to meet the higher standard.