Community manual annotation with Apollo (faqs)

How to upload BLAST hits to Apollo?

Run a BLAST job. In the results page for chromosomes, scaffolds, or contigs, click on 'GFF file for Apollo'. Save this file for later. Select the best hit In the pop-out window click on 'Browse Genome'

Automatic emails explained


Top tip: If you are splitting a gene model, you need to account for all children, tidy up after yourself!

Error in Gene Annotation

Q1. How to mark genes with no stop and/or no start codon?

Why don't you accept unmodified gene models?


We only use Apollo to receive your submissions of modification to gene structure, i.e., changes to the exon/

I just submitted my gene annotation. When will I see my submission incorporated in VectorBase?

  • VectorBase Apollo captures community gene annotations (i.e., corrections of gene structures) and other gene information such as metadata (for a few or group gene submissions), links your publications to the relevant gene(s) in the genome browser, allows gene deletions and repeat submissions too, follow this link for instructions.

How do I set a gene to pseudogene?


Use VectorBase web form called Gene Metadata following this link and select "

How do I decide on a gene name (symbol)?


  • Gene names (symbols) are few letters (such as "W" for the white gene, "INR" for insulin receptor, "SRPN18" for serpin 18 in Anopheles) and should be unique for each gene.
  • Gene descriptions are the "spelt out" version of the name (symbol), so "white", "insulin receptor" or "serpin 18" respectively, and are also unique for each gene.

How do I annotate a gene?


Apollo working space has the "User-created annotation tracks" on top and, below that an area were you can add evidence tracks. Activate the gene set track. Select, hold and drag a partial or full

How do I batch submit annotation metadata to VectorBase?


If you are submitting in batch, e.g., when you are annotating a gene family, you can fill an spreadsheet (e.g., Excel), rather than the web form for one gene at the time. Once you are done please send the file to Use the following 12 columns headings in the spreadsheet:

How do I add a comment to a gene?


Please type your comments in the "Gene Metadata" web form following this link.

Annotation Editors: Artemis and Apollo


There are a few annotation editors including Apollo and Artemis. Currently we only support Apollo for the VectorBase genome communities, which is also the tool of choice of the i5k community.


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