Bioinformatics, Vol 14, 384-390, Copyright © 1998 by Oxford University Press
AA Salamov, T Nishikawa and MB Swindells
MOTIVATION: 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. AVAILABILITY: The
prediction program, called ATGpr, and other data are available at
http://www.hri.co.jp/atgpr CONTACT: swintech@hri.co.jp
ARTICLES
Assessing protein coding region integrity in cDNA sequencing projects
Helix Research Institute, 1532-3 Yana, Kisarazu-shi, Chiba-ken 292, Japan.
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