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ORF-Length #2

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gedankenstuecke opened this issue Jul 4, 2012 · 1 comment

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bug

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gedankenstuecke commented Jul 4, 2012

Sometimes the lengths of the predicted nt & aa ORFs do not match up. If this is the case the nt-ORFs appear to be a bit longer (2-3 codons).

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gedankenstuecke commented Jul 5, 2012

Found two reasons for the behaviour:

ORFPredictor sometimes predicts ORFs which include a stop-codon which gets removed by OrthoMCL, thus rendering the alignments incompatible
Nucleotide-output of ORFPredictor will keep ambiguous nucleotide-codes if those are synonymous in terms of the resulting peptide-sequence. PAL2NAL crashes if ambiguity-codes are present.

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