Question: de novo annotation of plants genome
0
gravatar for hafiz.talhamalik
5 months ago by
Pakistan
hafiz.talhamalik230 wrote:

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

plants annotation genome • 162 views
ADD COMMENTlink modified 5 months ago by colindaven2.3k • written 5 months ago by hafiz.talhamalik230
1

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

ADD REPLYlink modified 5 months ago • written 5 months ago by lieven.sterck8.2k

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

ADD REPLYlink written 5 months ago by hafiz.talhamalik230

what do you understand with "annotated" ?

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

ADD REPLYlink written 5 months ago by lieven.sterck8.2k
2
gravatar for colindaven
5 months ago by
colindaven2.3k
Hannover Medical School
colindaven2.3k wrote:
  • 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
ADD COMMENTlink written 5 months ago by colindaven2.3k
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