General (faqs)

FAQ category.

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Can I use pictures posted in the Images section of VectorBase?


VectorBase has curated all available images and has included both the license and photographer into the image viewer on the site.

Nearly all of these images are in the public domain and freely available for non-commercial use. As an example, most images are from the CDC's Public Health Image Library and were taken by James Gathany, professional photographer for the US Centers for Disease Control and Prevention. The specimens were provided by Frank Collins (University of Notre Dame). Because these are US Government photographs, there are no copyright restrictions. However, if you use these photos, you should credit James Gathany as the photographer and directly contact him ( if you wanted to use any photographs for a commercial use, e.g., a DVD or a documentary. For the few images that are not from CDC/Gathany details are included with the image via the viewer.

When using images from this image gallery we kindly ask you to please acknowledge the source as 'VectorBase,'.

Do you have VectorBase introductory documentation or a tour?


Yes, we do. First, we suggest you go to VectorBase 'About' page, which gives you a quick and complete overview of data types and resources, with a Tour video and screen shots with sample queries and analyses, among other important information. If you want want to learn more, you may want to go to the tutorials page (in the Help navigation tab) and take a to look at the available tutorials in the 'General' category. If what you are looking for is more specific, we also have detailed tutorials for all our tools and resources, most with practice exercises and their corresponding answer keys.

Please, do not hesitate to email us to, if you have any questions or would like to provide us with feedback.

Do you have workshops on using VectorBase?


VectorBase hands-on workshops

We invite labs and institutes to host VectorBase workshops (demos and hands-on tutorials). You are free to select the topics you would like us to cover. If you are interested, please contact us at for more details.

Workshop at meetings/conferences

VectorBase staff also attend a number of meetings where we host workshops. These are usually connected with vector biology/tropical medicine meetings and are posted in our Newsletter and in the Meetings & Conferences section of our Forum.

FAQs and tutorials

Our FAQs, tutorials and our tour of VectorBase will give you an overview of what is possible.

Ensembl workshop

Another option is to participate to an Ensembl workshop which will give a good grounding in the tools we use (the ensembl genome browser and biomart data mining tool). More information about these can be found on this link

How to cite a community gene


Gene models are manually annotated by the community using Apollo from VectorBase. This allows all other members of the community to visualize changes instantly. Once a sufficient number of gene annotations has been accumulated for an organism, these new gene models are included in the next revision of the official gene set.

Cite a community gene or a manually annotated gene
Apollo has a gene annotation track in genome browsers to allow public display of ongoing Apollo edits. Apollo identifiers shown on the track are not stable identifiers and must not be used in publications referencing data as they may be deprecated without warning. If you require stable annotation IDs for Apollo gene model edits, please contact VectorBase directly and in your paper give the location of the gene (chromosome or scaffold, start, end).

Example of sentence: "The gene 'x' in the organisms 'y', was submitted to VectorBase as community annotation and is now available in the Apollo with the gene coordinates 'z', ... "

Gene metadata
The gene metadata, such as symbol (name), e.g., rpl2 and, a short functional description, e.g., ribosomal protein L2 should also be mentioned in your paper. If you are not sure on how to name a gene please follow these links for mosquitoes and other arthropods and for molluscans.

e.g.: Cornman et al. (2008). deposited in VectorBase a large set of Anopheles CPR genes and published an article citing the genes and their structures in Vectorbase. They named their genes but also provide in the Supplementary Material a list of the genes with their location on the Anopheles genome. Because many of their genes were already incorporated into the official gene set, they could also provide VB stable identifiers.

Why submit your genes to VectorBase?
VectorBase looks after the GenBank records of the genomic assemblies (and their gene annotation) for all VectorBase organisms. This means that when we update the official VectorBase gene set, we will also update the GenBank records so gene models will appear in GenBank. Although the GenBank record will not directly cite the submitter of a gene, it will link to the VectorBase Gene page, which will show that submitter.

When people have transcript sequences that are based on new sequencing, we anticipate that they will certainly want to submit that data directly to GenBank/EMBL/DDBJ; but we encourage them also to submit it to VB. Submission to VectorBase means that it will appear instantly in Apollo, and ensures that we are consistent in the use of gene symbols.

For information about how to cite VectorBase; how to cite a gene assembly and gene set and; how to cite an external data resource, please follow this link.

How to cite VectorBase


Cite VectorBase most recent paper

Giraldo-Calderón GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, VectorBase Consortium, Madey G, Collins FH, Lawson D. 2015. VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Research 43(Database issue):D707-13.

Reference a species geneset

VectorBase, (VectorBase most recent paper), <Species_name><isolate/strain> <Assembly, Gene set>.

Worked example

For example if you want to reference your usage of the Anopheles gambiae AgamP4.4 set of predictions you would use:

VectorBase, (Giraldo-Calderón et al 2015), Anopheles gambiae PEST, AgamP4.4.

Gene annotations

Providing in your publication VectorBase gene IDs allows for the easiest, most convenient and unequivocal strategy to identify the genes of interest. More information about the gene IDs can be found in this FAQ, Gene identifiers or gene IDs (e.g., AGAP + 6 digit number). In addition to provide the genes metadata, symbol (or name) and functional description, please make sure to submit this information (and the gene manual annotations if necessary) to upate VectorBase records and allow other users to find your genes with text searches too. Instructions for metadata submission for a few genes or in bulk can be found in the bottom portion Web Apollo's page and this related FAQ, How do I batch submit annotation metadata to VectorBase? We also strongly encourage you to work with the journal to provide the genome browser gene page link for each gene as shown in the example below.

Samples from the literature

Table 1. Summary of Ae. aegypti, An. gambiae and Cx. quinquefasciatus opsin genes.
Gene NCBI accession no. VectorBase gene ID Supercontig or Scaffold Base pair range on Supercontig/Scaffold No. amino acids No. exons Expression evidence (transcript, peptide) Predicted wavelength sensitivity range
Ae. aegypti
AaGPRop1 XM_001651947.2 AAEL006498 1.208 1,715,269–1,716,390 373 1 t, - Long
An. gambiae
Cx. quinquefasciatus


(...) The opsin protein sequences were submitted to VectorBase and comprise the official gene set for each species. Proposed gene names and putative functional annotations were also adopted by the database.'

Fragments extracted from: Giraldo-Calderoón GI, Zanis MJ, Hill CA. 2017. Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression. BMC Evolutionary Biology. 17:84

Of the canonical clock genes, period (agPER, AGAP001856), timeless (agTIM, AGAP008288), the transcriptional repressor cryptochrome 2 (agCRY2, AGAP004261), PAR-domain protein 1 (agPDP1, AGAP006376), and cycle (agCYC, AGAP005655) were found to be rhythmically expressed under LD and DD in both heads and bodies, consistent with findings in Ae. aegypti and Cx. quinquefasciatus (Fig. 2A, Fig. S5A, and Dataset S1) (18, 19).

Fragment extracted from: Rund SS, Hou TY, Ward SM, Collins FH, Duffield GE. 2011. Genome-wide profiling of diel and circadian gene expression in the malaria vector Anopheles gambiae. Proc Natl Acad Sci U S A. 108(32):E421-30.

How to subscribe to a mailing list


An overview of the mailing lists hosted a VectorBase is available here

Only the ones with a "Sign Up" link are open for subscription. The others are for contacting VectorBase with a recipient list of the developers.

Most of the VectorBase users are more likely to be interested in:
- news at vectorbase . org: receive information about VectorBase, main data releases or the newsletter.
- info at vectorbase . org: contact vectorbase to ask for information.

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