Assessing protein coding region integrity in cDNA sequencing projects.
BACKGROUND
In cDNA sequencing projects, it is vital to know whether the protein coding region of a sequence is complete, or whether errors have occurred during library construction. Here we present a linear discriminant approach that predicts this completeness by estimating the probability of each ATG being the initiation codon.


RESULTS
Because of the current shortage of full-length cDNA data on which to base this work, tests were performed on a non-redundant set of 660 initiation codon-containing DNA sequences that had been conceptually spliced into mRNA/cDNA. We also used an edited set of the same sequences that only contained the region following the initiation codon as a negative control. Using the criterion that only a single prediction is allowed for each sequence, a cut-off was selected at which discrimination of both positive and negative sets was equal. At this cut-off, 67% of each set could be correctly distinguished, with the correct ATG codon also being identified in the positive set. Reliability could be increased further by raising the cut-off or including homologues, the relative merits of which are discussed.


BACKGROUND
The prediction program, called ATGpr, and other data are available at http://www.hri.co.jp/atgpr


BACKGROUND
swintech@hri.co.jp
Salamov
A A
AA
Helix Research Institute, 1532-3 Yana, Kisarazu-shi, Chiba-ken 292, Japan.
Nishikawa
T
T
Swindells
M B
MB
D001483:Base Sequence; D018387:Codon, Initiator / Q000235:genetics; D019295:Computational Biology; D018076:DNA, Complementary / Q000235:genetics*; D016208:Databases, Factual; D006801:Humans; D016366:Open Reading Frames; D011506:Proteins / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D017422:Sequence Analysis, DNA
D018387:Codon, Initiator; D018076:DNA, Complementary; D011506:Proteins; D012333:RNA, Messenger