Explore the Apis mellifera genome
Example Data Points
For this
release we have chosen to display the data using Groups (or contigs).Use
the BLAST button in the menu, left, to locate
data, or enter the Group (e.g. Group6) and basepairs to jump
to, or scaffold (e.g. Group6.9) and basepairs to jump to.
A few example data points :
About the Honeybee genome
Assembly
This site presents an annotation of release 2.0 of the honeybee genome assembly [January 2005].
The honeybee genome sequence was determined by whole
genome shotgun at the Human Genome Sequencing Center at Baylor College of Medicine.
Annotation
The data comprises:
- Repeats which have been identified with:
- RepeatMasker using the Drosophila melanogaster repeat library
- RepeatMasker, with repeat consensi provided using an ab initio analysis kindly performed by Damian Keefe of the EBI's ENCODE project using the RECON repeat-finding package
- Repeat sequences identified by the ab initio analysis which were not found by the RepeatMasker's drosophila library
- Low complexity sequence identified with Dust.
- Ab initio gene predictions - which have been generated with Genscan and FGenesH
- Blast features - showing similarities to entries in Uniprot from a sensitive search against the genome.
- Gene predictions - These are grouped by confidence, and generated from a combination of evidence sources: honeybee-specific peptides, homology to Uniprot, and honeybee-specific ESTs. Lower confidence predictions are generated with homology to Uniprot only.
What's New in Ensembl 37
Apis mellifera News
- SSAHA2
Transcript-based SSAHA2 servers are now available for all species. Go to BlastView and select SSAHA2 from the Search Tool box.
- UniProt updates
Support has been added for variable splice UniProt records by adding an external db with a display label of "UniprotKB/SpliceVariant" to the external_db table on all databases.
Read more...
- GeneSeqalignView
This new view is based on GeneSeqView, with the added ability to align the given sequence with one or more species.
Read more...
- Bug fix to Transcript.pm
Transcript.pm; is_known() was returning true if the
transcript had a display_xref set, which is both incorrect and
inconsistent with the is_known() method in Gene.pm. The new behaviour is to return true if the transcript's status is KNOWN.
- Change to xref.display_label field
The width of xref.display_label has been extended to 128 characters to cope with the longer labels produced by gene name & GO term projection.
More news...
Statistics
| Assembly: |
Amel 2.0, Jan 2005 |
| Genebuild: |
Ensembl, May 2005 |
| Database version: |
37.2d |
| Known genes: |
3,239 |
| Novel genes: |
10,209 |
| RNA genes: |
86 |
| Genscan gene predictions: |
20,998 |
| Gene exons: |
136,802 |
| Gene transcripts: |
27,755 |
| Base Pairs: |
228,567,597 |
| Golden Path Length: |
224,720,104 |
| Most common InterPro domains: |
Top 40
Top 500 |
Links
A number of other sites are also displaying honeybee data or predictions. Notable sites are:
