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Fig. 2 | BMC Bioinformatics

Fig. 2

From: AlignWise: a tool for identifying protein-coding sequence and correcting frame-shifts

Fig. 2

Demonstration of how AlignFS corrects frame-shifts caused by deletions. For each alternative situation the original sequences are shown aligned to a homolog, how they are altered and the final ORFs in frame. Sequence 1 has a single gap, which is corrected by adding an ‘N’. Sequence 2 shows a 2 bp gap, corrected by adding 2 ‘N’s. Sequence 3 has a 4 bp gap, which is treated as a single gap followed by an in-frame deletion, as such it is corrected as in Sequence 1. The final example shows a longer gap where each end is treated in accordance to the reference frame (red boxes), as such the first codon is treated as in Sequence 2, and the end section is deemed in-frame. Alternating codons are shown in different shades of blue

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