Tools for annotating predicted genes?
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8 weeks ago
zack.saud ▴ 50


I've assembled a few fungal genomes and I usually do in-silico gene prediction with genemark ES and subsequently annotate the predicted proteins using a protein blast against the uniprot fungi database.

I then run Annie followed by GAG annotator to prepare the data for table2asn before submitting the annotated genome to NCBI. My problem is that they always flag up that some protein names are locus_tags of other proteins in the database. GAG or Annie seem to erroneuosly use the locus tag in the uniprot database as oppose to the protein name (either that or the locus tag is in place of the name in the database!).

Has anyone encountered this problem and have a good fix for it (or a better annotation tool)?

Many thanks in advance

Bioninformatics • 240 views
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Other annotation pipelines: LRSDAY has a well built annotation pipeline primarily for yeast genomes. It is for assembly etc as well but you can just plug in the assembly at the assembly step.

Otherwise I have used funannotate after braker gene prediction and have had no real problems


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