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BeeBase specifications

Information


Unique identifier OMICS_10641
Name BeeBase
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/Beebase

Maintainer


  • person_outline Christine Elsik

Publication for BeeBase

BeeBase citations

 (36)
library_books

A soft selective sweep during rapid evolution of gentle behaviour in an Africanized honeybee

2017
Nat Commun
PMCID: 5688081
PMID: 29142254
DOI: 10.1038/s41467-017-01800-0

[…] synonymous SNP variants within coding DNA sequence regions of the csd gene. Non-synonymy was determined via annotation with SnpEff version 4.2 using the Apis mellifera official gene set obtained from BeeBase. The combination of these non-synonymous coding SNPs thus represents allelic variants of the csd gene. A simple (ε = 0) median joining network was computed using the algorithm in PopArt, to a […]

library_books

Phosphoproteome Analysis Reveals Phosphorylation Underpinnings in the Brains of Nurse and Forager Honeybees (Apis mellifera)

2017
Sci Rep
PMCID: 5434016
PMID: 28512345
DOI: 10.1038/s41598-017-02192-3

[…] ed by retrieving the database of STRING v10 (http://www.string-db.org/). Then, we mapped these proteins to the benchmark sequences of A. mellifera proteome (version 3.2) downloaded from Bee Base (www.beebase.org) by BLAST search. Finally, we obtained 906,294 non-redundant PPIs in 8,336 proteins of A. mellifera. Thereafter, group-based prediction system (GPS) software package, was used to predict t […]

library_books

The Complex Demographic History and Evolutionary Origin of the Western Honey Bee, Apis Mellifera

2017
Genome Biol Evol
PMCID: 5381634
PMID: 28164223
DOI: 10.1093/gbe/evx009

[…] cedures were used because of the differences in the format of the raw sequence data from the Illumina and SOLiD platforms. All data were aligned to the A . mellifera reference genome version 4.5 (www.beebase.org; last accessed April 2014).We used the SAMtools/BCFtools packages () to call genotypes, using a quality score threshold of 30 for the data. We imposed some additional quality control filt […]

library_books

Transcriptome profiling of Diachasmimorpha longicaudata towards useful molecular tools for population management

2016
BMC Genomics
PMCID: 5059965
PMID: 27729028
DOI: 10.1186/s12864-016-2759-2

[…] ms the MUMMER software package, specifically Nucmer, [] and the Circos visualization tool [] were used. The Honey Bee Genome Sequencing Consortium assembly Amel_4.5 and Official Gene Set OGSv3.2 (www.beebase.org) and the NasoniaBase genome Assembly Nvit_1.0 (http://hymenopteragenome.org/nasonia/) databases were used. […]

library_books

Dusky like is required for epidermal pigmentation and metamorphosis in Tribolium castaneum

2016
Sci Rep
PMCID: 4735578
PMID: 26829909
DOI: 10.1038/srep20102

[…] ese insects, including T. castaneum (http://beetlebase.org/), A. gambiae (https://www.vectorbase.org/index.php), B. mori (http://silkworm.genomics.org.cn/), A. mellifera (http://hymenopteragenome.org/beebase/), A. pisum (http://www.aphidbase.com/aphidbase/), P. h. humanus (https://www.vectorbase.org/index.php) and National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov/gui […]

library_books

“Controlled, cross species dataset for exploring biases in genome annotation and modification profiles”

2015
PMCID: 4660258
PMID: 26693519
DOI: 10.1016/j.dib.2015.10.042

[…] except “match between runs” was enabled and data files were assigned their respective groups and fractions. The most recent honey bee Official Gene Set (OGS) protein database was downloaded from www.beebase.org (OGSv3.2). All other databases were downloaded from Uniprot proteomes (www.uniprot.org) on Feb. 5th, 2014. […]

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BeeBase institution(s)
Department of Biology, Georgetown University, WA, DC, USA; Department of Animal Science, Texas A&M University, College Station, TX, USA

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