1 / 1

VectorBase A home for invertebrate vectors of human pathogens vectorbase

VectorBase A home for invertebrate vectors of human pathogens http://www.vectorbase.org. info@vectorbase.org. Scope A resource center for invertebrate vectors of human pathogens , with an emphasis on community -driven data.

chaeli
Download Presentation

VectorBase A home for invertebrate vectors of human pathogens vectorbase

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. VectorBase A home for invertebrate vectors of human pathogenshttp://www.vectorbase.org info@vectorbase.org Scope A resourcecenter for invertebrate vectors of human pathogens, with an emphasis on community-driven data Species mosquitoes Anophelesgambiae, Aedesaegypti, Culexquinquefasciatus tick Ixodesscapularis & body louse Pediculushumanuskissing bug Rhodnius prolixus & tsetse fly Glossinamorsitans& additional Anophelinae and Aedes genomes, various fly genomes “VectorBase: a data resource for invertebrate vector genomics”. Lawson et al. Nucleic Acid Research, Database Issue, Jan. 2009 Data types • Genomic data • Genome browser • Genes, similarities, variations… • Comparative data • tBLAT, homologs, syntenies • Community annotation • Community gene models • Sequence data • Sequences in fasta format • Expression data • BASE • Published expression data • Community data • Ontology • Controlled vocabulary for: • GO terms • Tick anatomy • Mosquito anatomy • Insecticide resistance • Malaria • Population data • Population data • Meteorology and land cover data Community Engagement VectorBase privileges the contact with the community and has developed tools to capture community annotations and to map community data to vector genomes. • Manual annotation • Community Annotation Pipeline (CAP) • Integrate community manual annotation to gene sets. • 1- Submit data (mRNA sequence or gene name) • 2- Visualize in the genome browser (via DAS) • 3- Integrate in the gene set • Currently: • Community data mapping • Genome Annotation Viewer (GDAV) • Publish community EST/gene/protein • annotations, aligned to a genome. • Three files are required: • 1- Fasta sequences • 2- Sequence annotations • 3- Genome alignment Data access • Data mining • Genome Browser • Browse our Ensembl-like genome browser • BioMart • Use our sophisticated data-mining system • API • Programmatic access to MySQL databases • Download • Get sequences (fasta) or genes (gff3) • Bioinformatics tools • Blast • Sequence comparison vs. genome, gene, transcript or protein sequences. • HMMER • Build a HMMER model from a multiple sequence alignment (ClustalW) then use it to search our databases. The VectorBase project is funded by the U.S. National Institute of Allergy and Infectious Diseases (NIAID).We are extremely grateful to the community for submitting their data and giving their feedback.

More Related