Question: Eukaryotic gene annotation on gene predictions
gravatar for predeus
6 weeks ago by
predeus1.2k wrote:

Hello all,

I was wondering if there is a good tool for annotation of eukaryotic genes obtained by gene prediction, for example, by Braker pipeline (or any other gene prediction pipeline for that matter)? By annotation I mean basically blasting and hmm-scanning putative proteins against various databases.

There is Trinotate and Dammit for transcripts, and both work reasonably well for assembled transcriptomes. However they use transdecoder, which doesn't seem to like transcripts generated from gene predictions, because they generally lack UTRs.

Any suggestions would be appreciated!

ADD COMMENTlink modified 11 days ago by Biostar ♦♦ 20 • written 6 weeks ago by predeus1.2k

Since no one has suggested anything so far I will link Eric Normandeau's GAWN pipeline. There is also a biostars post for it: GAWN - Genome Annotation Without Nightmares

ADD REPLYlink written 6 weeks ago by genomax71k

Thank you, I'll give it a shot.

ADD REPLYlink written 6 weeks ago by predeus1.2k

Do you mean you look for a way to find gene functions? The common way to go is to run Interproscan. In one go you reach more than 20 different DB.

ADD REPLYlink written 11 days ago by Juke-342.7k

Wow, thank you. It takes a little while to get InterProScan running, but once you got it going, it's quite.. impressive.

ADD REPLYlink written 11 days ago by predeus1.2k

You can use Blast2GO for annotation.

ADD REPLYlink written 11 days ago by Mehmet490
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