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. 2015 Jan;43(Database issue):D707-13.
doi: 10.1093/nar/gku1117. Epub 2014 Dec 15.

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

Gloria I Giraldo-Calderón  1 , Scott J Emrich  2 , Robert M MacCallum  3 , Gareth Maslen  4 , Emmanuel Dialynas  5 , Pantelis Topalis  5 , Nicholas Ho  3 , Sandra Gesing  6 ; VectorBase Consortium; Gregory Madey  7 , Frank H Collins  8 , Daniel Lawson  9
Collaborators, Affiliations

VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases

Gloria I Giraldo-Calderón et al. Nucleic Acids Res. 2015 Jan.

Abstract

VectorBase is a National Institute of Allergy and Infectious Diseases supported Bioinformatics Resource Center (BRC) for invertebrate vectors of human pathogens. Now in its 11th year, VectorBase currently hosts the genomes of 35 organisms including a number of non-vectors for comparative analysis. Hosted data range from genome assemblies with annotated gene features, transcript and protein expression data to population genetics including variation and insecticide-resistance phenotypes. Here we describe improvements to our resource and the set of tools available for interrogating and accessing BRC data including the integration of Web Apollo to facilitate community annotation and providing Galaxy to support user-based workflows. VectorBase also actively supports our community through hands-on workshops and online tutorials. All information and data are freely available from our website at https://www.vectorbase.org/.

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Figures

Figure 1.
Figure 1.
A search workflow to find VectorBase data. (A) The search box is located in the top right-hand side of all VectorBase pages. Keywords for the queries can be typed in the box or the user can select to go to ‘Advanced Search’. (B) The word ‘pyrethroid’ could retrieve a results page like this one (Because VectorBase data is updated every 2 months, you may obtain different results). In the left-hand side is the ‘Filter Results’ box, the results can be filtered down when clicking on the domains, subdomains or species links. The filters can also be reset. In the center of the page are the results, linking to the page where they are displayed. (C) Alternatively, advanced search can be used to start with a more specific query, making use of the different menus and boxes.
Figure 2.
Figure 2.
A search workflow to find genes involved in metabolic pathways. (A) To find a gene of interest, either search or BLAST can be used. With search, the keywords can be the gene ID (e.g. AGAP004786), the gene name (e.g. pyruvate dehydrogenase) or the gene symbol (not available for this example). If using BLAST, click on the best transcript or protein hit and follow the ‘Browse Genome’ icon to the genome browser. (B) In the genome browser gene tab, there will be a link called ‘Pathways’. Click on this link to load the pathways table. Follow the link in the top hit, ‘aga00010’. (C) This is the glycolysis/gluconeogenesis cycle in the KEGG pathways. The notation and color coding of the pathways are described in the ‘Help’ link located in the top right-hand side.
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