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Table 1 Definitions of Discrepancy Types.

From: A novel approach to sequence validating protein expression clones with automated decision making

Discrepancies defined on nucleotide and polypeptide levels

Nucleotide changes

Polypeptide changes

Substitution

Silent substitution

 

Conservative substitution

 

Non-Conservative substitution

 

Missense substitution – any amino acid change

 

Truncation – inframe Stop codon

Frameshift deletion

Frameshift deletion

Frameshift insertion

Frameshift insertion

Inframe deletion

Inframe deletion

Inframe insertion

Inframe insertion

No Stop codon

Post-elongation

No Start codon

No Translation

Discrepancies defined on nucleotide level only

Discrepancies introduced by sequence ambiguity

   Start codon substitution

   Stop codon substitution

   Substitution in CDS region

   Frameshift insertion

   Inframe insertion

Discrepancies introduced by reference sequence ambiguity

   Substitution in CDS region

Flanking sequence region (5' and 3' regions described separately)

   Substitution – replacement of one base by another

   Deletion/insertion – deletion/insertion of several bases

   Ambiguous substitution – replacement of a base by ambiguous base

   Ambiguous insertion – insertion of ambiguous base

Discrepancy types for cDNA and flanking sequences defined at the nucleotide and polypeptide level by the Discrepancy Finder.