Beebase
Encyclopedia
BeeBase is an online bioinformatics database that displays data related to Apis mellifera, the European honey bee. It was developed in collaboration with the Honey Bee Genome Sequencing Consortium
.
In Feb 2007, BeeBase consisted of a GBrowse-based genome viewer and a CMap-based comparative map viewer, both modules of the Generic Model Organism Database
(GMOD) project. The genome viewer included tracks for known honey bee genes, predicted gene sets (Ensembl, NCBI, EMBL-Heidelberg), STS markers (Solignac and Hunt linkage maps), honey bee expressed sequence tags (ESTs), homologs in fruit fly
, mosquito
and other insects and transposable elements. The honey bee comparative map viewer displayed linkage maps and the physical map (genome assembly), highlighting markers that are common among maps.
Future enhancements planned for BeeBase are a QTL viewer and a gene expression
database. The genome sequence will serve as a reference to link these diverse data types.
Biological data and services available on BeeBase include:
Beebase organized the community annotation of the bee genome in collaboration with Baylor College of Medicine Human Genome
Sequencing Center http://www.genome.org/cgi/content/full/16/11/1329.
In the United Kingdom the National Bee Unit, part of the Food and Environment Research Agency, independently runs an information website under the name BeeBase https://secure.fera.defra.gov.uk/beebase.
Honey Bee Genome Sequencing Consortium
The Honey Bee Genome Sequencing Consortium is an international collaborative group of genomics scientists, scientific organisations and universities who are trying to decipher the genome sequences of the honey bee . It was formed in 2001 by American scientists...
.
In Feb 2007, BeeBase consisted of a GBrowse-based genome viewer and a CMap-based comparative map viewer, both modules of the Generic Model Organism Database
Generic Model Organism Database
The Generic Model Organism Database Project began as an effort to create reusable software tools for developing Model Organism Databases . MODs describe genome and other information about important experimental organisms in the life sciences...
(GMOD) project. The genome viewer included tracks for known honey bee genes, predicted gene sets (Ensembl, NCBI, EMBL-Heidelberg), STS markers (Solignac and Hunt linkage maps), honey bee expressed sequence tags (ESTs), homologs in fruit fly
Drosophila melanogaster
Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...
, mosquito
Mosquito
Mosquitoes are members of a family of nematocerid flies: the Culicidae . The word Mosquito is from the Spanish and Portuguese for little fly...
and other insects and transposable elements. The honey bee comparative map viewer displayed linkage maps and the physical map (genome assembly), highlighting markers that are common among maps.
Future enhancements planned for BeeBase are a QTL viewer and a gene expression
Gene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
database. The genome sequence will serve as a reference to link these diverse data types.
Biological data and services available on BeeBase include:
- DNADNADeoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
and protein sequence data - official bee geneGeneA gene is a molecular unit of heredity of a living organism. It is a name given to some stretches of DNA and RNA that code for a type of protein or for an RNA chain that has a function in the organism. Living beings depend on genes, as they specify all proteins and functional RNA chains...
set (developed by and hosted at Beebase) - genomeGenomeIn modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
browser - linkage maps
- server to search the honey bee genome using BLASTBLASTIn bioinformatics, Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences...
Beebase organized the community annotation of the bee genome in collaboration with Baylor College of Medicine Human Genome
Human genome
The human genome is the genome of Homo sapiens, which is stored on 23 chromosome pairs plus the small mitochondrial DNA. 22 of the 23 chromosomes are autosomal chromosome pairs, while the remaining pair is sex-determining...
Sequencing Center http://www.genome.org/cgi/content/full/16/11/1329.
In the United Kingdom the National Bee Unit, part of the Food and Environment Research Agency, independently runs an information website under the name BeeBase https://secure.fera.defra.gov.uk/beebase.