de novo annotation of plants genome

Question

[hafiz.talhamalik]

any suggestion of tool for annotation of plant genome ? data I have is of plant for which no prior genome/annotation is available. I did the denovo assembly and now I want to perform annotation. suggestion would be appreciated

[lieven.sterck]

This is a quite common question and has been asked (and answered) before. Did you put in some effort in finding a solution yourself? (eg, have a look at the similar questions section on the right here)

annotation of a plant genome is in essence not much different from any other eukaryotic genome, so you could expand your search or at least have a look at what people do (or asked) for other species as well.

You could also track down a few publications of plant genomes and read what people did for those annotation -wise

[hafiz.talhamalik]

i came across few tools like maker-p but most of the genomes they used were already annotated.

[lieven.sterck]

what do you understand with "annotated" ?

Maker-P is exactly to be used to annotated 'raw' genomic sequences

Answer 1

[colindaven]

• Maker and or Maker P is good. You can predict genes de novo without prior info .... and or use protein to genome mappings as well.
• if you have de novo transcripts eg from RNA-seq you can use these in Maker and or in GMAP with GFF3 output

Answer 2

[sagnik]

Hello Hafiz,

We have developed a gene annotator called FINDER which can annotate eukaryotic genomes using short-read RNA-Seq reads and protein sequences. It is completely automated and requires no manual intervention. FINDER also runs BRAKER to incorporate predicted genes in the repertoire. You can access the paper from FINDER and the software from here GitHub.

Thank you.

[Denis]

Hi! I'm wondering about a minimal number of different RNA-Seq libraries for different tissues and conditions we have to prepare for successful annotation with FINDER? What if we would have just a single RNA-Seq library? We have to use only a paired-end RNA-Seq libraries within FINDER, am i right?