VectorBase

VectorBase^[1]^[2] is one of the five Bioinformatics Resource Centers (BRC) funded by the National Institute of Allergy and Infectious Diseases (NIAID), a component of the National Institutes of Health (NIH), which is an agency of the United States Department of Health and Human Services. VectorBase is focused on invertebrate vectors of human pathogens working with the sequencing centers and the research community to curate vector genomes (mainly genome annotation).

Genomes covered in the VectorBase database

Tools available through the VectorBase site

Genome browser
Community annotation system
Microarray and gene expression repository
Controlled vocabularies for anatomy,^[5] insecticide resistance and vector-borne diseases (malaria and dengue fever)
BLAST searches for all covered genomes

References

^ Lawson, D; Arensburger, P; Atkinson, P; Besansky, NJ; Bruggner, RV; Butler, R; Campbell, KS; Christophides, GK; et al. (2007). "VectorBase: a home for invertebrate vectors of human pathogens". Nucleic Acids Research. 35 (Database issue): D503–5. doi:10.1093/nar/gkl960. PMC 1751530. PMID 17145709.
^ Lawson, D; Arensburger, P; Atkinson, P; Besansky, NJ; Bruggner, RV; Butler, R; Campbell, KS; Christophides, GK; et al. (2009). "VectorBase: a data resource for invertebrate vector genomics". Nucleic Acids Research. 37 (Database issue): D583–7. doi:10.1093/nar/gkn857. PMC 2686483. PMID 19028744.
^ Nene, V; Wortman, JR; Lawson, D; Haas, B; Kodira, C; Tu, ZJ; Loftus, B; Xi, Z; et al. (2007). "Genome sequence of Aedes aegypti, a major arbovirus vector". Science. 316 (5832): 1718–23. Bibcode:2007Sci...316.1718N. doi:10.1126/science.1138878. PMC 2868357. PMID 17510324.
^ Holt, RA; Subramanian, GM; Halpern, A; Sutton, GG; Charlab, R; Nusskern, DR; Wincker, P; Clark, AG; et al. (2002). "The genome sequence of the malaria mosquito Anopheles gambiae". Science. 298 (5591): 129–49. Bibcode:2002Sci...298..129H. CiteSeerX 10.1.1.149.9058. doi:10.1126/science.1076181. PMID 12364791. S2CID 4512225.
^ Topalis, P; Tzavlaki, C; Vestaki, K; Dialynas, E; Sonenshine, DE; Butler, R; Bruggner, RV; Stinson, EO; et al. (2008). "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase". Insect Molecular Biology. 17 (1): 87–9. doi:10.1111/j.1365-2583.2008.00781.x. PMID 18237287. S2CID 8618269.

External links

vectorbase.org
Bioinformatics Resource Centers The NIAID page describing the goals and activities of the BRCs
Pathogen Portal Hub site for the five BRCs; provides summary information

VectorBase genome browsers

Aedes aegypti genome browser at VectorBase
Anopheles gambiae genome browser at VectorBase
Culex quinquefasciatus genome browser at VectorBase
Ixodes scapularis genome browser at VectorBase
Pediculus humanus genome browser at VectorBase
Rhodnius prolixus genome browser at VectorBase

[1] Lawson, D; Arensburger, P; Atkinson, P; Besansky, NJ; Bruggner, RV; Butler, R; Campbell, KS; Christophides, GK; et al. (2007). "VectorBase: a home for invertebrate vectors of human pathogens". Nucleic Acids Research. 35 (Database issue): D503–5. doi:10.1093/nar/gkl960. PMC 1751530. PMID 17145709.

[2] Lawson, D; Arensburger, P; Atkinson, P; Besansky, NJ; Bruggner, RV; Butler, R; Campbell, KS; Christophides, GK; et al. (2009). "VectorBase: a data resource for invertebrate vector genomics". Nucleic Acids Research. 37 (Database issue): D583–7. doi:10.1093/nar/gkn857. PMC 2686483. PMID 19028744.

[3] Nene, V; Wortman, JR; Lawson, D; Haas, B; Kodira, C; Tu, ZJ; Loftus, B; Xi, Z; et al. (2007). "Genome sequence of Aedes aegypti, a major arbovirus vector". Science. 316 (5832): 1718–23. Bibcode:2007Sci...316.1718N. doi:10.1126/science.1138878. PMC 2868357. PMID 17510324.

[4] Holt, RA; Subramanian, GM; Halpern, A; Sutton, GG; Charlab, R; Nusskern, DR; Wincker, P; Clark, AG; et al. (2002). "The genome sequence of the malaria mosquito Anopheles gambiae". Science. 298 (5591): 129–49. Bibcode:2002Sci...298..129H. CiteSeerX 10.1.1.149.9058. doi:10.1126/science.1076181. PMID 12364791. S2CID 4512225.

[5] Topalis, P; Tzavlaki, C; Vestaki, K; Dialynas, E; Sonenshine, DE; Butler, R; Bruggner, RV; Stinson, EO; et al. (2008). "Anatomical ontologies of mosquitoes and ticks, and their web browsers in VectorBase". Insect Molecular Biology. 17 (1): 87–9. doi:10.1111/j.1365-2583.2008.00781.x. PMID 18237287. S2CID 8618269.

[1]

[2]

[3]

[4]

[5]

v t e Bioinformatics
Databases	Sequence databases: GenBank, European Nucleotide Archive, DNA Data Bank of Japan and China National GeneBank Secondary databases: UniProt, database of protein sequences grouping together Swiss-Prot, TrEMBL and Protein Information Resource Other databases: BioNumbers, Protein Data Bank, Ensembl, InterPro, KEGG, and Gene Ontology Specialised genomic databases: BOLD, Saccharomyces Genome Database, FlyBase, VectorBase, WormBase, Rat Genome Database, PHI-base, Arabidopsis Information Resource, GISAID and Zebrafish Information Network
Software	BLAST Bowtie Clustal EMBOSS HMMER MUSCLE PANGOLIN SAMtools SOAP suite TopHat
Other	Server: ExPASy Rosalind (education platform)
Institutions	Broad Institute Computational Biology Department (CBD) Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI) Database Center for Life Science (DBCLS) DNA Data Bank of Japan (DDBJ) European Bioinformatics Institute (EMBL-EBI) European Molecular Biology Laboratory (EMBL) Flatiron Institute J. Craig Venter Institute (JCVI) Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG) US National Center for Biotechnology Information (NCBI) Japanese Institute of Genetics Netherlands Bioinformatics Centre (NBIC) Philippine Genome Center (PGC) Scripps Research Swiss Institute of Bioinformatics (SIB) Wellcome Sanger Institute Whitehead Institute
Organizations	African Society for Bioinformatics and Computational Biology (ASBCB) Australia Bioinformatics Resource (EMBL-AR) European Molecular Biology network (EMBnet) International Nucleotide Sequence Database Collaboration (INSDC) International Society for Biocuration (ISB) International Society for Computational Biology (ISCB) Student Council (ISCB-SC) Institute of Genomics and Integrative Biology (CSIR-IGIB) Japanese Society for Bioinformatics (JSBi)
Meetings	Basel Computational Biology Conference‎ ([BC²]) European Conference on Computational Biology (ECCB) Intelligent Systems for Molecular Biology (ISMB) International Conference on Bioinformatics (InCoB) International Conference on Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB) ISCB Africa ASBCB Conference on Bioinformatics Pacific Symposium on Biocomputing (PSB) Research in Computational Molecular Biology (RECOMB)
File formats	CRAM format FASTA format FASTQ format NeXML format Nexus format Pileup format SAM format Stockholm format VCF format GFF format GTF format
Related topics	Computational biology List of biobanks List of biological databases Molecular phylogenetics Sequencing Sequence database Sequence alignment
Category Commons

Genomes covered in the VectorBase database

Tools available through the VectorBase site

See also

References

External links