Eukaryotic gene annotation on gene predictions
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2.8 years ago
predeus ★ 1.8k

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!

annotation eukaryotic gene prediction • 789 views
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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

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Thank you, I'll give it a shot.

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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.

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

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You can use Blast2GO for annotation.

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