If you have single DNA bases at the beginning (or end) of the DNA sequence
there have to be corresponding proteins in the protein sequence. Otherwise translation
will fail.
Normally, if you use codon start other than 1 during translation, a 'X' will be inserted
into the resulting protein sequence. That X is required by the re-aligner to skip up to
3 DNA positions, while it is trying to find the correct ORF.
Missing X's at protein sequence start are a very common cause,
for various kinds of error messages from the re-aligner.
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