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Data Sets

Apis mellifera Genome Sequences

 


Current Assembly

Amel_4.5

 

Data Usage Policy:
Genomes and predicted gene sets for the following species are not yet published: Bombus terrestris, B. impatiens, Apis florea, A. dorsata, and A. mellifera (latest assembly Amel_4.5).These sequences are provided to the public pre-publication to allow research on individual genes to proceed faster than the genome analysis would allow.  They are covered by the Ft. Lauderdale (1) and later Toronto (2) agreements whereby the data producers make the data available and state their intent to publish analyses, the data users ask permission to use the prepublication data and cite the appropriate source, and the journals and reviewers make sure that articles are published following the guidelines.  Release to GenBank and Ensembl and similar repositories does not constitute publication. Please contact us if you wish to use these sequences in published analyses.
References:
1. Sharing Data from Large-scale Biological Research Projects: A System of Tripartite Responsibility. Report of a meeting organised by the Wellcome Trust and held on 14-15 January 2003 at Fort Lauderdale, USA.
2. Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature. 2009 Sep 10;461(7261):168-70.
 
How to Cite:
Please cite the use of this database as: Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera. Munoz-Torres MC, Reese JT, Childers CP, Bennett AK, Sundaram JP, Childs KL, Anzola JM, Milshina N, Elsik CG. Nucleic Acids Research (2011) 39(suppl 1): D658-D662 doi: 10.1093/nar/gkq1145

Amel_4.5 at NCBI NCBI's FTP (invertebrates) public site for A. mellifera.
OGS not yet available for download Data from assembly Amel_4.5 of the Apis mellifera genome have not yet been published. All may browse these data on HGD's Honey Bee Genome Browser, but files for download will be available after the consortium manuscript is published.  The consortium is actively working on the manuscript. 

 

Previous assemblies

Amel_2.0


Amel_2.0_scaffolds.fa.gz These are the scaffolds from the second assembly for the Apis mellifera genome, in FASTA format.

amel_OGSv1.0 This is the first release of the Apis mellifera Official Gene Set, built on assembly Amel_2.0.
amel_OGSv1.0_pep.fa.gz Contains all predicted proteins in this gene set. Previously named Amel_release1_OGS_pep.fa.gz.
amel_OGSv1.0_transcript.fa.gz

Contains all translated regions in this gene set. Previously named Amel_release1_OGS_cds.fa.gz.

amel_OGSv1.0.gff.gz

Contains all gene annotations, in a gff version 3 file. Previously named Amel_release1_OGS_on_assembly2.gff.gz.

amel_OGSv1.1 This is the second release (previously known as "PreRelease 2") of the Apis mellifera Official Gene Set; built on assembly Amel_2.0.
amel_OGSv1.1_pep.fa.gz Contains all predicted proteins in this gene set. Previously named Amel_pre_release2_OGS_pep.fa.gz.
amel_OGSv1.1_transcript.fa.gz Contains all translated regions in this gene set. Previously named Amel_pre_release2_OGS_cds.fa.gz.
amel_OGSv1.1.gff.gz

Contains all gene annotations, in a gff version 3 file. Previously named Amel_pre_release2_OGS_on_assembly2.gff.gz.

amel_abinitio This is ab initio set for Apis mellifera was built on assembly Amel_2.0.
amel_abinitio_pep.fa.gz Contains all predicted proteins in this gene set. Previously named Amel_abinitio_pep.fa.gz.
amel_abinitio.gff.gz

Contains all gene annotations, in a gff version 3 file. Previously named Amel_abinitio_on_assembly2.gff.gz.

Amel_3.0

Not available for download Due to its short-lived nature, we do not recommend using Amel_3.0 and have not made these files available. Should you require to use them, please let us know.

Amel_4.0

Amel_4.0_scaffolds.fa.gz These are the scaffolds from the fourth assembly for the Apis mellifera genome, in FASTA format.

Chromosome SuperScaffolds These are chromosome SuperScaffolds, built on A. mellifera assembly Amel_4.0.

mapped_to_Amel_4.0 Gene models from amel_OGSv1.0 and manual annotations were mapped to assembly Amel_4.0.
amel_manual_annotations_mapped_to_Amel_4.0.gff.gz Manual annotations submitted by the honey bee research community, mapped to A. mellifera genome assembly Amel_4.0.
amel_OGSv1.0_mapped_to_Amel_4.0.gff.gz

Gene models from amel_OGSv1.0, mapped to A. mellifera genome assembly Amel_4.0.

Download Apis mellifera Sequences by ID

You may download Apis mellifera sequences from the following sources using IDs as queries. Click here for examples of proper search IDs for each category.

Previous resleases from Baylor Previous genome releases from the Human Genome Sequencing Center at Baylor College of Medicine (HGSC-BCM)
GBrowse at BeeBase

Visit HGD's GBrowse pages for all available data for Apis mellifera.