Question: Porting genome annotations from virus RefSeq to new strain: any web tools?
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gravatar for ch504
18 months ago by
ch5040
ch5040 wrote:

I have about 80 dsDNA virus genomes which I have either mapped or de novo assembled (depending on read depth) using CLC Genomics Workbench. I now need to annotate the genomes.

References sequences and published genomes with annotations exist for my sample set; I need to port over (presumably with some manual curation) those annotations so I can upload to GenBank.

Unfortunately, I've changed jobs and no longer have access to CLC or a computing cluster - it's just me and my PC. If I wait for my old group's bioinformatician to do the annotations for me, this data might wait until the heat death of the universe.

Thus I am looking for an online or PC-compatible tool that will allow me to port annotations over. I've had recommendations for GLUE http://tools.glue.cvr.ac.uk/#/home and VIGOR http://www.jcvi.org/vigor/ but neither seems suitable for dsDNA viruses, and I don't need a de novo annotation - the ones that exist will be fine once ported across.

I feel like uGENE probably has this functionality but I just can't work out how one would achieve this. Suggestions welcomed - I'm sure someone has solved this problem and I'm eager to avoid re-inventing the wheel.

ADD COMMENTlink modified 18 months ago by Joseph Hughes2.7k • written 18 months ago by ch5040
1
gravatar for Joseph Hughes
18 months ago by
Joseph Hughes2.7k
Scotland, UK
Joseph Hughes2.7k wrote:

RATT is a tool developed by Sanger which works well for annotation transfer from strains and closely related species. You will need an embl formatted file with the annotations and your fasta formatted sequence to start off with.

Another tool worth trying but I haven't used is GATU for which there is a web server somewhere (can’t currently find it) as well as a GUI. See documentation here: https://virology.uvic.ca/help/tool-help/quick-start-pages/gatu-quick-start/

ADD COMMENTlink written 18 months ago by Joseph Hughes2.7k
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