 |
 |
v22.34d.1 Update |
 |
|
|
|
|
Ensembl human v22.34d.1 is a minor update, made to accompany the chicken release.
The new/updated human data in release 22 are:
 Core database
- Affy probe hits added as "misc features"
- RefSeq mRNA links (NM_ identifiers) have been added for each of the protein
links (NP identifiers)
Compara database
- New homology analysis including chicken and honeybee
- Orthologue analysis was extended so that now all species pairs have
putative orthologues. For cross-phylum analyses (e.g. mosquito vs
C.elegans), only BRH (best reciprocal hit) were calculated.
- Protein families recalculated so to include the latest SWISSPROT and SPTREMBL
|
|
|
|
|
|
Schema changes in v22 |
|
|
|
|
|
Core database
2 new tables (translation_attrib & transcript_attrib) added, for
handling exceptional cases in transcripts/translations, e.g
selenocysteins and RNA edits. Data to populate these tables is still
in preparation.
The "code" column in the "misc_set" table was expanded from
varchar(15) to varchar(25).
SNP database
"hapmap_snp" column added to the "RefSNP" table to provide a boolean
flag indicating whether this RefSNP has been typed in the HapMap
project or not.
Compara database
added column "chr_strand" to "member" table which copies Gene and
Transcript strandedness (1 or -1) from the core databases
added column "locator" to "genome_db" table which stores a locator string
which describes how to get a DBAdaptor for the corresponding core
database. It is used in pipeline production, but set to an empty string
for release.
|
|
|
|
|
|
|
New features in v22 |
|
|
|
|
|
MultiContigView
We are pleased to announce a new comparative genomics view for Ensembl:
MultiContigView. This page displays simultaneous contigviews for
multiple species, aligned by compara genomic alignment blocks. e.g. MultiContigView.
You can enter the page on a location (from one species), along with the
name of one or more additional species. The initial alignment is
selected as the best available between the two species, interpolated from
the DNA align features in the compara database. MultiContigView is
linked to from ContigView (via Compara DNA align features), and GeneView.
This is the initial release of this page, and we are planning a number of
improvements. We would be appreciative of any feedback you might have,
good or bad, about this display.
|
|
|
SNPView
Now displays a link to the HapMap
Project if the SNP has been typed in HapMap.
|
|
|
Site Maps
The site maps have been reworked, and are now generated dynamically from
the available data. This means they are more up-to-date, more accurate,
and more useful for navigating the site. [more].
|
|
|
ContigView
Affy probe track added. The Affymetrix probe hits stored in the core
database are now displayed as a track on ContigView. This track can be switched on and off from the 'Features' menu.
Transcript tracks are now collapsible. Transcript tracks can be collapsed down into genes by clicking the red "-" symbol to the left of the track name.
|
|
|
Homo_sapiens 