Are undetermined "n" nucleotides in the V-REGION counted as mutated nucleotides in IMGT/V-QUEST analysis?
In IMGT/V-QUEST analysis, undetermined "n" nucleotides in the V-REGION are counted as mutated nucleotides.
Their number is explicitly indicated in the results as "V-REGION uncertain nt nb":
- below the Result summary in 'A. Detailed view' display,
- in a column in 'B. Synthesis view' display,
- in 'nt-sequences' in 'C. Excel file' (equivalent to 'nt-sequences' CSV file of IMGT/HighV-QUEST results)
How can sequences with frameshifts and STOP-CODON be 'productive' in IMGT/(High)V-QUEST?
Two examples are detailed in the pdf
In both cases the sequences have a large deletion (65 nt and 49 nt, respectively) which is not a multiple of 3.
and the translation beyond the deletion is indeed a frameshift with stop codons.
However in IMGT/HighV-QUEST, the tool by default searches and corrects the insertions/deletions, which means that the tool provides
a translation in-frame (because it ignores the nt 'c' (codon 48 of seq1) or the 2 nt 'ct' (codon 21 of seq2).
As this translation is without STOP-CODON and that the junction is in-frame, the functionality assigned by the tool is 'productive'. Practically this information may be useful
if the large deletions are experimental artefacts.