Is it possible to use CESAR2.0 to align protein sequences to a target genome?

[xiekunwhy]

Hi,

I want to do homolog-base gene predition. And the protein sequences are obtained from orthordb10, and is it possible to use CESAR2.0 to align these protein sequences on to my assemblies and do gene predition. How to do that if it is possible.

Best,
Kun

[MichaelHiller]

Hi Kun,

CESAR needs an annotation for the species you want to use as the reference. Then you need to produce a genome alignment between the reference and the query.

If the reference has no annotation, you can align orthodb proteins to create an annotation. But ideally transcriptomics data should be used to obtain a highly-accurate and highly-complete annotation for the reference.

CESAR is reference-based, so the better the input, the better the output.

Best
Michael