Frameshifts

What is frameshift?
If a gene is far shorter than others it is a candidate for a frameshift. If it's short you must extend it so it reaches full size. Alternatively it is a pseudogene coming from a gene duplication event.

Sequencing error Sometimes when sequencing some bases could be lost or added, and so shift the reading frame.

How do we correct?
Our pipeline will be able to find and take the decision to put two genes together if they are too short, and save this into a log file. But in the hard case where one of two gene-copies are very much shorter than the other one, it could be a good idea to leave the decision to the user. Another possibility could be to just simply remove the gene copy that aligned worst. Sometimes with frameshifts a correction could be to just go back and find the methionine and put together the full size gene. Remark! Double orthologs could in fact be the same frameshifting gene and not a sign of gene duplication. But remember there are large grey areas and there the decision is best done by the user.

HAL/Giovanni
They have completely ignored the fact that grey areas exist.

Also
In "Bartonella?" the bacteria can use a frameshiftfenomena to regulate gene-expression.