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v28.2c.1 Update |
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This release includes a lot of new and updated data including the addition of
the Xenopus tropicalis genome, additional linkage disequilibrium (LD) data for human, new mouse genes, and updated SNP sets for human, dog and Anopheles.
Ensembl Archive sites
Ensembl have also released the first two Ensembl Archive sites:
http://Nov2004.archive.ensembl.org
http://Dec2004.archive.ensembl.org
The Ensembl Archive sites have been set up so it is possible to have a
permanent link for at least two years to pages from a
particular release (e.g. version 26 from November 2004) in Ensembl.
These links will be suitable for referring to Ensembl pages in publications.
For more information about the Ensembl Archive sites see
http://archive.ensembl.org.
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New data in v28 |
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Comparative genomics (ensembl_compara_28_1)
Proteins:
New putative orthologues for mouse and X. tropicalis with all other species
New family data for mouse and X. tropicalis
New human, mouse and rat paralogues
New family build due to mouse and Xenopus tropicalis
DNA:
D. melanogaster
- against Anopheles TRANSLATED_BLAT
- against Bee TRANSLATED_BLAT
C. familiaris
- against Fugu TRANSLATED_BLAT
- against Tetraodon TRANSLATED_BLAT
- against Danio TRANSLATED_BLAT
- against Chicken TRANSLATED_BLAT
- UCSC BLASTz with Mouse
Synteny of X. tropicalis
X. tropicalis transBLAT with human (Hs35)
X. tropicalis transBLAT with mouse (Mm33)
X. tropicalis transBLAT with rat (Rn3b)
X. tropicalis transBLAT with dog (Cf1)
X. tropicalis transBLAT with chicken (Gg1)
X. tropicalis transBLAT with fugu (Fr2a)
X. tropicalis transBLAT with zebrafish (Dr4)
X. tropicalis transBLAT with T.nigroviridis (Tn1)
Mart databases
Ensembl now uses BioMart, the successor to EnsMart. For this reason the Mart database has now been split into four databases:
ensembl_mart_28_1
snp_mart_28_1
vega_mart_28_1
sequence_mart_28_1
BioMart has a new API. The BioMart code has been designed specifically
to facilitate query-oriented data integration and to use external datasets.
The installation is now highly customisable and uses a registry
for external databases and an XML-based configuration system
for dataset configuration.
For more information on the BioMart project see
www.ebi.ac.uk/biomart.
The Ensembl installation documentation is being updated to reflect these changes.
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Anopheles gambiae
Variation database (anopheles_gambiae_variation_28_2c)
fixed strain information
added missing SNP mapping
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Schema changes in v28 |
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Core database
Added analysis_description table
Modified external_db table: RefSeq entry modified to be RefSeq_dna and RefSeq_peptide
Removed removed binary constraint on dbprimary_acc in xref table
Altered EMBL and Genbank dumping scripts to include / gene line
Schema patch
The 27 to 28 patch file is available in CVS at
ensembl/sql/patch_27_28.sql to enable schema 27 databases to be patched to schema 28 without the need to re-download the data.
Compara database
Addition of:
MAX_ROWS = 1000000000 AVG_ROW_LENGTH = 60;
to the genomic_align table as it passed the default table space limit.
Addition of a new core table definition related to the analysis table
in order for the new AnalysisAdaptor to work with compara
CREATE TABLE analysis_description (
->analysis_idint(10) unsigned NOT NULL,
-> description text,
-> display_label varchar(255),
->
-> KEY analysis_idx( analysis_id )
-> );
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New features in v28 |
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Pop-up menus on images
Pop-up menus now appear on images when you click on a feature rather
than when you move over a feature. The old action is still available
on displays which are configurable.
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MartView
The new features of MartView include the ability to:
combine filters from two datasets
define fasta headings
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Chromoview/Karyoview
These two views now accept the same three types of user data:
file upload
a URL
data pasted directly into the form
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FeatureView
FeatureView is now configurable so you can select
the colour and style of pointers
the size and layout of chromosomes
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Anopheles_gambiae 