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Integr8 :
Access to complete genomes and proteomes
| e.g. "coli", "9606" |
e.g. "ras1", "P22981", "GO:0007257", "GO:mitosis" |
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The Integr8 web portal provides easy access to integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.
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Integr8 data can also be accessed via the
Integr8 FTP site.
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New to Integr8?
The user guide will show you how to make the most of the data provided
by Integr8. Alternatively,
you may choose to start
browsing the data.
We value your feedback! Please send us your comments.
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| News |
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Current Status |
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Focal Point |
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A new DAS service has been established, mapping RNA evidence for proteins present in the Integr8 proteome sets onto the protein sequence. DAS is a lightweight protocol enabling easy integration and visualisation of sequence-based annotation, and the new Integr8 service provides access to information identifying the regions of predicted protein sequences where a matching RNA molecule has been sequenced (more...)
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A complete list of Integr8 species and their proteome status can be found on the current status page of the
Integr8 documentation.
This release of Integr8
(release 102)
was built from UniProt release 15.10
and InterPro release 23.0
and was released on Mon, Nov 16, 2009.
The summary chart below shows the types of species currently held within Integr8.
Click on the chart to browse species in Integr8 by taxonomic classification. |
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Intentions for Ensembl Genomes Release 4
Intentions for Ensembl Genomes Release 4
The following intentions have been declared for the 4th release of Ensembl Genomes, due 12th January 2009.
Software
- upgrade to using Ensembl 57 software.
- new Pan Compara database incorporating e57 vertebrate genomes and including stable identifiers for gene trees.
Bacteria
- Updates to existing clades (based on latest data from UniProtKB and EMBL) including additional species.
- Three new clades including data from the genera Buchnera, Borrelia and Wolbachia based on data from EMBL and UniProtKB.
- Functional genomics databases showing mapping of Affymetrix probes for Escherichia and Streptococcus.
- Updated peptide and DNA compara database.
- Updated BioMart
Fungi
- Updates to existing databases to include GOSlim references.
- Update to A. nidulans to reflect changes to gaps used in assembly.
- Updates to S. pombe based on latest data from UniProtKB and EMBL.
- New core database for Neurospora crassa based on data from EMBL and UniProtKB.
- DNA compara database for Aspergillus species.
- Updated BioMart.
Protists
- Updates to P. knowlesi and P. vivax based on latest data from UniProtKB and EMBL.
- Update patches for P. falciparum (repeats and gene symbols).
- New core databases for P. yoelii, P. berghei and P. chabaudi using gene data from PlasmoDB.
- New core database for Dictyostelium discoideum using gene data from DictyBase.
- Variation database (dbSNP import for P. falciparum).
- Updated peptide compara database.
- DNA compara database for plasmodia.
- Updated BioMart.
Metazoa
- Updated Aedes aegypti core database
- Updated Anopheles gambiae core database
- New core database for P. humanus humanus.
- New functional genomics databases for mosquitoes.
- New functional genomics database for C. elegans.
- New variation database for D. melanogaster.
- Updated peptide compara database.
- New DNA compara databases for Drosophilids and mosquitoes.
- Updated BioMart.
Plants
- Updated variation database for A. thaliana to include Oxford indels and data on read coverage.
- Updated variation database for V. vinifera to include data on read coverage.
- Updated BioMart.
Ensembl Genomes is being developed as the successor project to Integr8, which will be phased out in the near future.
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History |
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Latest species |
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GAS top 10 |
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Funding
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Integr8 has been funded by the European Commission: from March 2006 - February 2009 under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme, and from January 2002 - June 2005 as the TEMBLOR, contract number QLRI-CT-2001-00015 under the RTD programme "Quality of Life and Management of Living Resources"
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