 |
 |
New data in v19.34a.1 |
 |
|
|
|
|
Build 34a Geneset Update
Ensembl v19 contains an updated gene build on the NCBI34 assembly
released in v18. The majority of gene structures from build 34 are
unchanged, but 200-300 are improved predictions produced as a result of
corrections in our gene building software. The build contains 23531 gene
predictions with 31609 transcripts, including 1744 pseudogenes.
We are continuing to improve our prediction methods and expect to
produce another NCBI34 rebuild early in 2004.
The 34a version increment indicates a data update without a change in
assembly.
In addition to the updated genebuild, Human 19.34a.1 contains:
Improved archived identifier data in the core
database
Filtered SNP set from dbSNP 117. The new SNP
database contains 276000 fewer SNPs, as these were mapped to the
alternate HSC_TCAG which is not represented in Ensembl.
Additional homology data from the Compara
database.
|
|
|
Schema changes in v19 |
|
|
|
|
|
Compara
Addition of two columns, "dn" and "ds" in the homology table
These columns are filled only for some paired species, i.e. human/mouse,
human/rat, mouse/rat and elegans/briggsae. For the other paired species,
the ds values obtained were saturated and were viewed as unreliable. For
those cases, the ds and dn columns are null.
|
|
|
|
|
|
New Features in v19.34a.1 |
|
|
|
|
|
GeneDAS
This release sees a further extension and incorporation of the DAS
protocol into Ensembl. For a long time DAS has been used to include
external annotations, including user's own data, on ContigView displays.
This concept has now been applied to the GeneView display, enabling
external annotations on specific genes to be incorporated into the page.
The first dataset to be included is SwissProt literature references for
genes. [ e.g. ] This is only the beginning for GeneDAS, and we are working on
providing a number of data sources, as well as enabling users to display
their own gene annotations.
|
|
|
GeneSNPView
GeneSNPView is a new gene-centric SNP display. This page, linked from
GeneView, shows details of SNPs and Pfam domains in, or close to, the exons
of the transcripts of a particular gene. The SNP data includes their
location, alleles, classification, and effects on the different
transcripts. [ e.g. ]
|
|
|
ChromoView
A new "tool" page has been added this release. ChromoView enables the
customisable display of feature frequency data against a single
chromosome or a karyotype. The data can be provided by cut-and-paste,
by file upload, or by providing a URL of a datafile. ChromoView accepts
a variety of formats, including simple tab- or space-delimited, PSL, BED
and GFF.
ChromoView is available for all species with an assembly mapped to
chromosomes. [ e.g. ]
Please let us know if you find ChromoView useful, or have suggestions for
improvements.
|
|
|
GeneView Orthologues
GeneView now displays further details from the Compara database.
Orthologue predictions show how they were selected (Best Reciprocal Hit
or Reciprocal Hit based on Synteny around BRH) and give a value for dN/dS
where available.
|
|
|
ContigView tracks
New Anopheles Gap track (Decorations menu,
Gaps). This track displays the location of gaps both between and
within scaffolds.
Ensembl & Vega transcript tracks now show
include the type of transcript in the labels below each transcript.
This can be switched off by selecting "Concise labels" in the
Decorations menu.
The BLAST hit track now shows additional match
details.
|
|
|
Webcode redesign
Release 19 sees the continued rollout of the redesigned webcode.
Updated pages in this release are FASTAView, ExonView, MapView,
AnchorView and SNPView.
|
|
|
MartView updates
Number of transcripts per gene is available for
export and filtering.
Exons are flagged as constitutive or alternative
depending on their presence or not in all the transcripts of a gene.
New data available on orthologous gene
relationships
See the EnsMart homepage for more details of Mart
updates.
|
|
|
Homo_sapiens 