Community manual annotation with Web Apollo (faqs)

Displaying 1 - 10 of 13

Annotation Editors: Artemis, WebApollo and CLC


There are a few annotation editors such as CLC, Web Apollo or Artemis. Currently we only support Web Apollo for the VectorBase genome communities.

If you have a question about Web Apollo please refer to its tutorial page which includes a user manual, tutorial slides, a video tutorial and practice exercises among other resources.

Generic Feature Format Version 3 (GFF3) file format


GFF3 files are nine-column, tab-delimited, plain text files.

  • Column 1: sequence ID
  • Column 2: source, e.g., VectorBase, Ensembl, Genbank.
  • Column 3: type of feature
  • Columns 4 & 5: start and end coordinates of the feature
  • Column 6: in score, E-values are used for sequence similarity features and P-values for ab initio gene prediction features.
  • Column 7: The strand of the feature. + for positive strand, - for minus strand, and . for features that are not stranded. In addition, ? can be used for features whose strandedness is relevant, but unknown.
  • Column 8: For features of type "CDS", the phase indicates where the feature begins with reference to the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed from the beginning of this feature to reach the first base of the next codon.
  • Column 9: A list of feature attributes in the format tag=value. Multiple tag=value pairs are separated by semicolons.

You can download GFF3 files from VectorBase or you can create them de novo. For the later case you have three options:

  • Manually with a text editor that does tabs, e.g., NotePad++ or TextWrangler.
  • With Excel, save the file as “Tab Delimited Text (.txt)” (shown below).
  • Write a script, e.g., with Perl or Python.

For more information about the GFF3 file format go to:

This page includes an online GFF3 validator and a detailed description of each column of this file format.

How do I add a comment to a gene?


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

How do I add a gene name (symbol) to a NEW gene model I just created?


Use the "Gene Information Capture" web form following this link. The gene ID should be the same as the one you used in the NEW Web Apollo gene model. It should be unique. We suggested using "yourusernameX", where 'X' would be a number, e.g., ggiraldo1. Use Web Apollo Information Editor with the only purpose of giving a name to the gene, please leave all the other fields of the Editor empty.

Then fill in the rest of the VectorBase web form as you would normally for an existing gene model. Follow this link for instructions of how to do that.

Please follow this link for the FAQ about gene IDs.

How do I add a gene name (symbol) to an EXISTING gene model?


Please use VectorBase web form called "Gene Information Capture" following this link.

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 Excel spreadsheet, 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:

  1. Timestamp: dd/mm/yyyy
  2. Species
  3. VectorBase gene ID: e.g, AGAP000002. In the absence of a VectorBase gene ID give scaffold and base pair coordinates, e.g. scaffold_1:1010-4549.
  4. Gene status: Use this section to confirm the gene structure, mark as a pseudogene or delete the prediction completely.
    • Approve gene structure
    • Set as pseudogene
    • Delete

    Justification: Indicate in a few words why you think this gene should be deleted/set as pseudogene or which evidences helped you decide its structure is correct (e.g. "Supported by RNA-seq data", "similarity with Drosophila protein XYZ")

  5. Gene symbol: Indicate the gene symbol. It should be short and unique to each gene (e.g. "SRPN18" for serpin18).
  6. Justification: Indicate in a few words how you've attributed this gene symbol (e.g. "Based on similarity to Drosophila Female sterile (2) Ketel (Fs(2)Ket) gene")

  7. Gene synonyms: Indicated any synonyms for the locus
  8. Description: If should be relatively short (e.g. "Serpin", "Ion channel receptor").
  9. Justification: Indicate in a few words how you've attributed this description (e.g. "Based on similarity to topless Drosophila gene")

  10. PubMed ID: e.g., 25510499
  11. Submitter Name
  12. Email
  13. Review: Use Review to state that the prediction is not correct but the submitter does not have enough information/time/inclination to correct it at this time, this can be a ToDo list for interested parties.
  14. Comments/Notes: Leave any other comments you have about this gene (e.g. "Truncated gene, other part on scaffold scfxxxxxx", split GMOY123456[1/2] or, merge GMOY123456-GMOY123457).

How do I create a new gene?


Web Apollo working space has the "User-created annotation tracks" on top and, the "Evidence tracks area" below it. Select, hold and drag a partial or full transcript or gene model, from the evidence area to the user created area to create a new gene.

You can see how this is done in Web Apollo video tutorial, just go to minutes 19:15 to 20:50, following this link.

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.
  • If you want to give a gene name (symbol), we recommend you pick up a meaningful one (e.g. "SRPN", for consistency with Anopheles) and since it's a gene family, add a number (e.g."SRPN11"). The gene description would be "serpin1".
  • At the end of the annotation process, we will send this list to everyone for assessment and make sure there aren't any duplicates.
  • Please follow this link for the FAQ "Rules and conventions for naming genetic features in mosquitoes (and other arthropod vectors)" for more details about this topic.

How do I delete a gene?


Please use VectorBase web form by following this link. Select "delete" as the action to perform on this gene and explain in a few words why you think it should be deleted (not need for details).

How do I open a GFF3 file in WebApollo?


As shown on slide # 20 of the tutorial and minutes 12:35 to 13:53 of the video tutorial, the Web Apollo window has three menu items on top, click the one called File to upload a GFF3 file. Follow this link for both the tutorial slides and the video.


Subscribe to Community manual annotation with Web Apollo (faqs)