FRAME - DETECTION OF GENOMIC SEQUENCING ERRORS

Motivation: The underlying error rate for genomic sequencing sometimes results in the introduction of artificial frameshifts and in-frame st op codons into putative protein encoding genes. Severe errors are then introduced into the inferred transcripts through mis-translation or p remature termination. Results: We describe a system for screening segm ents of DNA for frameshift and in-fame stop errors in coding regions. The method is based on homology matching using blastx to compare all s ix reading frames of the query nucleotide sequence against selected pr otein sequence databases. Fragments of protein matching neighbouring r egions of the query DNA are united and extended laterally to define ca ndidate open reading frames, within which, frameshifts and stops are i dentified. Suitable targets include prokaryotic or other intron-free g enomic sequence and complementary DNAs. As an example of its use, we r eport here two frameshifted ORFs that deviate from the original TIGR s equence annotations for the recently released Helicobacter pylori geno me.