Insertions and deletions cause frameshifts when translating DNA sequences to protein sequences -- RDP FrameBot detects and corrects these frameshift errors. Given a DNA read and a set of known protein sequences, it produces frameshift-corrected protein and DNA sequences and an optimal global-local protein pairwise alignment.
You can adjust the length cutoff (after alignment) and the percent identity cutoff to filter out non-target reads. FrameBot has been tested and pre-configured for several important functional genes (see more details in help). If your gene is not in the list, you need to provide your own set of protein target sequences (limited to 200).