[maker-devel] Annotation of a new variant within a species

[Lior Glick]

Hello,

I am trying to annotate multiple  variants of tomato. While a good
annotation of the reference genome is available, I have denovo-assembled
other variants of the same species and wish to annotate them.
Most MAKER documentation refers to annotation of a new species, while using
transcripts and proteins from either the exact same sample (individual) or
from "an alternate organism", so I'm not sure what to do in this case,
where I am annotating various samples from the same species. I have two
questions:

1. Regarding transcripts data, how should I use transcripts from other
variants of the same species? Namely, should I use the est or the altest
parameter? What is the actual difference in behavior?

2. Is there a way to incorporate gene models (in gff format) from the
reference annotation? I expect high similarity in my assembled variants,
but not identity in terms of content and coordinates, so neither pred_gff
nor model_gff sound like what I need, as far as I understand.
I could also use the reference annotation and sequence to extract cDNA and
provide them as EST data. Is this the way to go? It feels like some
information on introns might be lost this way.

Would highly appreciate your answers to these questions or any other advice.

Thank you very much!
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