v1.6
An integrated data warehouse for the Hymenoptera Genome Database
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Please contact us if you would like any additional template queries or if you have a concern about a query not completing.
Given a gene id, retrieve the coding sequences.
Given a gene id, retrieve GO terms.
Retrieve gene ids and their aliases for an organism. Multiple gene sets may be returned if the gene source is not selected. See the Data Source page for gene source names.This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given a Gene id retrieve transcript id(s). This is especially useful for RefSeq gene sets,
Given a UniProt id, retrieve gene id.
Given an Alias ID, retrieve Gene ID, optionally constrained by gene source. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given a gene id, retrieve homologues from either the OrthoDB or HGD-Ortho data set. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD. If your output has inparalogs (multiple homologous genes per species), narrowing the taxonomic group may reduce the number of inparalogs. The last common ancestor options available for OrthoDB are Apoidea, Formicidae, Hymenoptera and Holometabloa. See the Taxonomy tab above for the HGD-Ortho options.
Given a gene id or symbol, retrieve chromosome and coordinates.
Given a gene id or symbol, retrieve transcript ids and locations and exon coordinates.
Retrieve all homologues for an organism for either the OrthoDB or HGD-Ortho data set. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD, but you can modify it using the pulldown menu.
Given a Gene Symbol, retrieve GO terms.
Given a gene id, retrieve gene symbol and description.
Given a gene symbol, retrieve proteins (UniProt).
Retrieve gene ids and UniProt protein ids from a gene set. Multiple gene sets will be retrieved for organisms that have more than one gene set, unless the optional constraint to specify gene set is used. Output will include only ids that correspond to a UniProt id.
Given a gene id, retrieve gene alias id. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given the gene source and organism, retrieve all gene ids. This template is useful for creating a whole-gene-set background population for the enrichment widgets if you save the output as a list.
Given a gene symbol, retrieve gene id.
Given a gene id, retrieve pathways.
For a given organism, retrieve gene ids from the selected gene set mapped to UniProt protein ids. Only gene ids that map to UniProt ids will be retrieved. Mappings are from UniProt.
Given a GO term, retrieve genes annotated with that GO Term for a selected organism.
Given a non-A.mellifera organism, retrieve all A. mellifera orthologues with their pathways.
Given a gene id, retrieve gene symbol and go terms.
Given a gene id, retrieve database cross reference id.
Given a Gene ID, retrieve Drosophila melanogaster orthologue (recriprocal best hit).
Retrieve all gene symbols and descriptions from a RefSeq gene set for a specified organism.
Retrieve genes located on a chromosome for an organism.
Given a gene alias id, retrieve genes and gene database cross references. This is useful for converting from old to new OGS. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given an OGS gene id, retrieve database cross reference id (RefSeq) with symbols and descriptions.
Retrieve all proteins (UniProt) for a particular organism.
Given a gene id, retrieve gene alias ids and database cross references. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Given a CDS ID, retrieve gene id and symbol. This is useful for a list of CDS retrieved from a regions search.
Given an organism, retrieve all genes that have go terms, along with their GO terms.
Given a NCBI gene ID, retrieve protein and coding sequences.
Given a RefSeq or GenBank protein id, retrieve protein sequences.
Given a transcript id, retrieve transcript alias id.
Given an organism, retrieve all transcript ids with their gene ids and alias ids. Multiple gene sets may be retrieved if the optional gene source constraint is not selected. This template can be used for A. dorsata, A. florea, A. mellifera, B. impatiens, B. terrestris, L. humile, P. barbatus, W. auropuncata.
Retrieve gene ids for an organism. Multiple gene sets may be returned if the gene source is not selected. See the Data Source page for gene source names.
Retrieve all genes and their chromosomal locations for an organism.
Given a transcript ID, retrieve gene ID and symbol.
Given a transcript alias id, retrieve transcript and gene id. This template should be used for A. echinatior, C. biroi, C. floridanus, D. novaeangliae, E. Mexicana, H. laboriosa, H. saltator, L. albipes, M. quadrifasciata, M. rotundata, S. invicta.
Given an organism, retrieve gene ids that have pathways, along with their pathways.
Given a genome assembly version, retrieve primary chromosome IDs used in HymenopteraMine, alternative IDs and chromosome lengths. In the results table, the ID that should be used in the Regions Search is called "Chromosome ID".
Given a gene id, retrieve publications.
Retrieve all publications with gene ids from an organism.
Given an orthologue cluster ID, retrieve genes.
Retrieve Drosophila melanogaster orthologues (reciprocal best hit) for an organism.
Given a Gene ID, retrieve Drosophila melanogaster orthologue (reciprocal best hit) and its pathways. There will be no output if there is no recipocal best hit or no pathways.
Given a gene id, retrieve transcript ids and protein ids from the gene source.
Given a RefSeq or GenBank gene id, retrieve associated protein sequences (from RefSeq or GenBank).
Given a transcript id, retrieve transcript alias id. This template can be used for A. echinatior, C. biroi, C. floridanus, D. novaeangliae, E. Mexicana, H. laboriosa, H. saltator, L. albipes, M. quadrifasciata, M. rotundata, S. invicta.
Given a gene id, retrieve homologues in the selected organism from the HGD-Ortho data set. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD. If you find too many inparalogs with Holometabola, you can select a narrower taxonomic group that contains both species. See the Taxonomy tab above for Last Common Ancestor choices for HGD-Ortho.
Given a transcript id from RefSeq or GenBank, retrieve the coding sequence.
Given an orthologue cluster ID, retrieve protein sequences. The sequences can be exported in fasta format. You can filter the "Is Representative" column for "true" to select one protein sequence per gene.
Given a transcript alias id, retrieve primary transcript id and gene id, gene database cross reference id, and gene description. This template can be used for A. echinatior, C. biroi, C. floridanus, D. novaeangliae, E. Mexicana, H. laboriosa, H. saltator, L. albipes, M. quadrifasciata, M. rotundata, S. invicta.
Given an orthologue cluster ID, retrieve coding sequences. The sequences can be exported in fasta format. You can filter the "Is Representative" column for "true" to select one coding sequence per gene.
Given a gene id, retrieve homologues from the HGD-Ortho data set. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD. If your output has inparalogs (multiple homologous genes per species), narrowing the taxonomic group may reduce the number of inparalogs. See the Taxonomy tab above for the Last Common Ancestor options for HGD-Ortho.
Given a gene id, retrieve homologues from the OrthoDB data set. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD. If your output has inparalogs (multiple homologous genes per species), narrowing the taxonomic group may reduce the number of inparalogs. The Last Common Ancestor options available for OrthoDB are Apoidea, Formicidae, Hymenoptera and Holometabola.
Given a gene id, retrieve homologues in the selected organism from the OrthoDB data set. By default the Last Common Ancestor is set to Holometabola, the broadest taxonomic group in HGD. If you find too many inparalogs with Holometabola, you can select a narrower taxonomic group that contains both species. The choices for Last Common Ancestor for OrthoDB are Apoidea, Formicidae, Hymenoptera and Holometabola.