About VectorBase Tutorials


This video will give you a 6 minute tour of VectorBase. VectorBase is an NIAID Bioinformatics Resource Center providing genomic, phenotypic and population-centric data to the scientific community for invertebrate vectors of human pathogens.


What is VectorBase?

VectorBase is a Bioinformatics Resource Center (BRC) focused on invertebrate vectors of human pathogens. VectorBase is one of four Bioinformatics Resource Centers providing web-based resources to the scientific community, supporting basic and applied research on organisms causing emerging or re-emerging diseases, or considered potential agents of biowarfare or bioterrorism. All VectorBase resources are made freely available to the research community under the GNU General Public License.

This project receives Federal funds from the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Department of Health and Human Services (HHS), under Contract No. HHSN272201400029C to the University of Notre Dame. The current principal investigators are F. Collins, S. Emrich (University of Notre Dame) and D. Lawson (Imperial College London).


Data types and sources

Available data types

VectorBase contains a variety of data types, including reference and variant genome sequence, structural annotations (e.g., gene models, protein domains), functional annotations, and phenotypic and population data for traits such as insecticide resistance. Some of these data are imported from external databases and others are computed derived from primary data. For example, with every VectorBase release we re-calculate homology relationships i.e., paralogs and orthologs, the effect of sequence variations on protein coding sequences, and the mapping of array probes to updated gene models.

Data sources

We strongly encourage you to talk to us prior to data submission. VectorBase incorporates data from public archival databases for nucleotide sequence (i.e., ENA, GenBank and DDBJ) and other databases including dbSNP, KEGG pathway, UniProt, InterPro, RefSeq, ArrayExpress, the Sequence Read Archive (SRA), the European Variation Archive (EVA), and the Gene Ontology (GO). VectorBase would be happy to broker submissions from individual researchers to the major data centres and discuss incorporation into our resource of non-archivable data including but not limited to relevant metadata.

Genome Annotation in VectorBase

VectorBase can provide support to researchers interested in particular genes, and to researchers working on whole genomes. Small scale manual annotation of genomes is supported using the Web Apollo system, while if you are developing a reference genome sequence we can collaborate with you to perform large scale automated genome annotation. Our genome annotation pipeline uses evidence based and ab initio computational approaches to generate high quality genome annotation that is continually updated to reflect the latest community research.

Recently we have started to use orthology relationships to project gene descriptions (e.g., serpin 7) from species that have been extensively studied to other closely-related but less well described species. We do not project gene names, e.g., GPRop13. Details about this process and the species where the descriptions are being propagated can also be found in the tutorial link above.

Genomes

This is the list of all genomes hosted in VectorBase


What can you do with VectorBase?

VectorBase provides information for numerous vector species, access to Data resources for those organisms, and a variety of Tools to analyze these data sets. You can use the data we host or upload your own data for private analyses. Some sample queries and analyses are:

  • Search, analyze, visualize and compare organisms genome and various data types (called tracks), such as SNPs, RNA-seq and mass spectrometry data, with the Genome Browser, e.g., kdr mutation L1014S/F in Anopheles gambiae para gene
  • Full-screen view

    Full-screen view

    Full-screen view

  • Download complex data sets, including nucleotide and protein sequences with BioMart, e.g., Culex quinquefaciatus coding genes on supercontig3.1:1458134-2603182
  • Full-screen view

  • Use Search to look for a gene with its VectorBase gene ID e.g., Ixodes scapularis ISCW005498. The use of symbol (name) and description (function) is not recommended.
  • Full-screen view

  • Perform a query with BioMart to dowload protein sequences from a well annotated gene family. With ClustalW run a multiple sequence alignment of the proteins and use the “Send to HMMer” link to discover homologous genes in your species of interest. e.g., Discover odorant receptor (OR) genes in Aedes albopictus, using the ones from Aedes aegypti
  • Full-screen view

    Full-screen view

  • Using previously published microarray and/or RNA-seq data to study patterns of differential expression in an organism under different experimental conditions, e.g., An. gambiae immunity genes in mosquitoes feed with different species of Plasmodium
  • Full-screen view

  • Use BLAST to locate where in a genome a set of primers bind, e.g., Ae. aegypti lysosomal aspartic protease (LAP) gene
  • Full-screen view

  • Use Galaxy with your data or previously published raw sequencing data, to run a SNP calling pipeline and predict population(s) polymorphisms**
  • Full-screen view

  • Map visualization of population biology data, e.g., insecticide susceptibility status for An. gambiae s.l. in West Africa (Benin, Ghana, Guinea, Liberia, Mali, Nigeria and Senegal)
  • Manually update gene annotations* using Web Apollo
  • Full-screen view

  • And many other research questions with our tools and resources, or with the data we host but using external bioinformatic tools.


Saving and sharing - data and analyses

You can save and compare your analyses with colleagues, including:
  • Genome Browser custom tracks
  • BLAST, ClustalW and HMMer job results
We are currently working to improve the capabilities of your user account, please send us your suggestions for features that you would like to have.


Your results and publications

Screenshots or images taken from VectorBase can be freely used in your presentation slides, in your thesis document, journal or news media publication, or any other scientific document. If you use VectorBase resources please cite both our most recent paper and the paper where the data was originally published as shown in these two links: how to cite VectorBase and data submission and access policies.


Help, documentation and discussion

We provide a set of Help pages that include Tutorials and other background information. You can also participate in discussions with us and other members of our user community through our Forum or social media pages on Facebook and Twitter. We also welcome feedback through our Contact form.

Please explore the site and let us know if you have any questions or suggestions, we love to hear from you!


People


Accessibility

The VectorBase BRC continually strives to make sure our resource is Section 508 compliant. In the event that the website, documentation or training material cannot be accessed, please inform us and we will quickly provide an alternative form of this material or training at no charge.


*For Web Apollo a user account is needed. Other tools can be used without registration.


** Some user requests could exceed the capacity of VectorBase servers because either the fundamental analysis is too large, or because there is contention for resources with other users of the system. If your analysis fails please contact us with details of the analysis you were performing and the error encountered so that we can investigate the cause.