Bioinformatics, Vol 14, 367-371, Copyright © 1998 by Oxford University Press
NP Brown, C Sander and P Bork
MOTIVATION: The underlying error rate for genomic sequencing sometimes
results in the introduction of artificial frameshifts and in-frame stop
codons into putative protein encoding genes. Severe errors are then
introduced into the inferred transcripts through mis-translation or
premature termination. RESULTS: We describe a system for screening segments
of DNA for frameshift and in-frame stop errors in coding regions. The
method is based on homology matching using blastx to compare all six
reading frames of the query nucleotide sequence against selected protein
sequence databases. Fragments of protein matching neighbouring regions of
the query DNA are united and extended laterally to define candidate open
reading frames, within which, frameshifts and stops are identified.
Suitable targets include prokaryotic or other intron-free genomic sequence
and complementary DNAs. As an example of its use, we report here two
frameshifted ORFs that deviate from the original TIGR sequence annotations
for the recently released Helicobacter pylori genome. AVAILABILITY: The
tool is accessible via the URL http://www.sander.ebi.ac.uk/frame/. CONTACT:
brown@ebi.ac.uk.
ARTICLES
Frame: detection of genomic sequencing errors
1European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, CB10 1SD, UK. brown@ebi.ac.uk
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