Can you use high quallity annotation of very closely related to annotation novel genome

Question

[robert.murphy]

We have a genome with accompanying high quality annotations from a collaborator and I am wondering if it is possible to use this to annotate our novel genomes directly?

I am aware I can train Augustus through Braker2 using protein hints with a protein.fa from this "reference" genome but it is possible to literally use the annotation from the reference and apply them to our novel genome with some homologous variable accounting for potential slight variations?

[Juke34]

MAKER is well suited for this task.

[robert.murphy]

Does MAKER not use protein and RNA-seq hints from the genome being annotated to inform its annotation? I guess using a closely related strain hints would also work? But lets say they are not available I am unfamiliar with how I could use the reference annotations with MAKER?

[Juke34]

I would extract proteins and transcripts from your annotation and give them to MAKER. Have a look here: https://github.com/NBISweden/workshop-genome_annotation_elixir/blob/master/lectures/Structural_annotation_MAKER.pdf I think the concept is the same as mapping an annotation forwards to a new assembly.

You should read Genome Annotation and Curation Using MAKER and MAKER-P, Current Protocols in Bioinformatics,2014.

There are other tools, see this parper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450745/ CESAR is very interesting