VectorBase.org: Over A Decade of Service to the Vector Community.

Frank Crisione, Ph.D.

Frank Crisione, Ph.D., Postdoctoral Research Associate, Institute for Bioscience and Biotechnology Research, University of Maryland College Park. More about the Author

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VectorBase, one of the most popular bioinformatic resources for vector genomics, has recently undergone a version update and plans to provide stronger and faster computing power to the vector community. As described in a recently published paper in Nucleic Acids Research by Giraldo-Calderón et al. (2014), the website has revamped its interface, increased the amount of hosted genomic data, and implemented a myriad of new tools to increase the ease and efficacy of bioinformatic analysis.

Upon first opening Vectobase.org, users should notice the change in layout – all the old VectorBase features are still accessible with the addition of some new features. The website’s makeover reorganized data categories to improve the flow of navigation and added a search function allowing for faster access to information based on keywords. Simple searches can be performed through the search-bar utilizing keywords. More complex search capabilities will be made possible through BioMart and are currently under development. These features would allow a user to perform an advanced search based on a field queries or searches based on ontology terms. Users will now also find that personal accounts can be created that will store tool parameters and past analysis through the use of the Drupal management system.

Screen Shot of VectorBase's homepage

Screen Shot of VectorBase’s homepage

The NIH and NIAID funded bioinformatic resource launched 11 years ago. Rising from the need to host genomic data from newly sequenced insect vectors of parasites and pathogens, the bioinformatic resource center has grown to host the genomes of 35 organisms to date.

VectorBase has grown to host more than just genomes. New data has been added to the population biology (PopBio) browser that incorporates data from field and insecticide resistance studies. More thorough expression analysis is made possible with the expansion in the number of transcriptomes hosted based on RNA-seq and microarray data for various organisms. Downstream analysis of genomic data can also be aided by the pathway information available in the genome browser.

Gene annotations initially generated from ab initio assembly or predicted by MAKER can now be edited by users and will be included in future version updates. The addition of this capability harnesses the research power of the vector community to create more accurate and comprehensive databases.

New tools of the website include Galaxy, expression maps, and an Ontology Browser . Galaxy is a suite of computational tools that can perform a variety of bioinformatic analysis such as next gen sequencing alignments. The expression maps are tools for visualizing gene clusters based on their experimentally verified expression data. This system is integrated with BioMart, allowing for data from gene clusters to be retrieved and further analyzed.

VectorBase Tools Screen Shot.

VectorBase Tools Screen Shot.

VectorBase is consistently developing and expanding its ontologies that relate to vectors of disease. The Ontology Browser is the first of its kind, combining web-based navigation with the capability to handle large ontologies with speed and efficiency. The browser is also coupled with a powerful search engine, increasing the ease of navigation.

Future updates of VectorBase look to hold many more enhancements to the bioinformatic services provided to the vector community. VectorBase has proposed a mission to expand its genetic data on population variation and insecticide resistance as well as increase the capabilities of Galaxy to improve the ease of RNA-seq analysis. It is anticipated that VectorBase will continue strengthen the bridge of research that connects disease vectors and pathogens in the years to come.

Take a look at Giraldo-Calderón et al. (2014) for all of the details about what’s new in VectorBase.

Giraldo-Calderon GI, Emrich SJ, MacCallum RM, Maslen G, Dialynas E, Topalis P, Ho N, Gesing S, Consortium V, Madey G, Collins FH, Lawson D (2014) VectorBase: an updated bioinformatics resource for invertebrate vectors and other organisms related with human diseases. Nucleic Acids Res  10.1093/nar/gku1117

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