News and Events
   
  Ensembl release 40
  Writer : Seyeon Weon     Date : 10-07     Hit : 10838    
  트랙백 주소 : http://www.bioinformatics.pe.kr/gnuboard/bbs/tb.php/news/16
We are pleased to announce the new Ensembl website www.ensembl.org ,
the main new features in this release are below.
(See http://www.ensembl.org/Multi/newsview?rel=40 for more detail).


Highlights for this Release:

  New 2x Genomes.
  ---------------

We have developed a new gene building pipeline which works with
the new low coverage genome data in mammalian
species, producing a good set of genes (around 16,000) in
Elephant, Armadillo, Tenerec and Rabbit. These gene builds
present this challenging data in a useful manner, allowing people
to work in a gene-centric manner with these organisms and making
it easier to integrate this data with the finished and high coverage
mammalian genomes.

  Gene Trees
  ----------

The gene level comparative genomics has moved towards Gene level
trees, allowing a far richer insight into the evolution of genes,
including the timing of duplication events. The resulting trees
have been projected into pairwise relationships between genes,
distinguishing different types of orthologous relationships
(one2one, one2many, many2many) and timing intra-species paralogs.

The Gene Trees are visualised in a new display at:

A simple mammalian ortholog group:

http://www.ensembl.org/Homo_sapiens/genetreeview?db=core;gene=ENSG00000050730

A far more complex, metozoan Gene family with multiple members per  species:

http://www.ensembl.org/Homo_sapiens/genetreeview?db=core;gene=ENSG00000137601


Currently the 2x genomes are not integrated with the Gene Trees, but
will be in the October release.


  New 6x Genomes: Rhesus Macaque and Stickleback
  ---------------------------------------------

Two new important genomes have been released as full Ensembl gene builds
Rhesus monkey has been updated to the more recent assembly with an
improved gene build and Stickleback (Gasterosteus aculeatus), a model
fish has been released with a Gene Build based on both protein  similarity
and extensive EST evidence.



Full Release notes follow:


New Data
---------

* New species:
  6 new species (including 4 low coverage genomes):
    - the yellow fever mosquito (Aedes aegypti),
    - stickleback
    - 2x elephant
    - 2x armadillo
    - 2x tenerec
    - 2x and rabbit.

* New genebuilds:
  for rhesus macaque, rat and fly.


* Vega (manual annotation)
  New Vega for mouse.

* Ditag data
  Added for human and mouse (DAS track on ContigView).

* Affy mappings
  1 additional Affy array has been mapped to human, 7 for mouse, 4  in rat and 2 in yeast


* Minor patches for 3 species
  Anopheles
  Mouse
  C. savignyi


* Expression data
  Zebrafish: new ZFIN data


* Variation data

  Human: dbSNP 126, on NCBI36 (genotype data from dbSNP 125).

  Affymetrix genechip array 100K and 500K data track added to  Contigview.

  Mouse: dbSNP 126, on NCBIm36.
        Sanger-called SNPs and multiple strain tables added to Mart.

  Rat: updated to match new genebuild.

  Dog: allele table updated with data from Broad Institute.


* Core databases
  Non-schema patches applied to core data patches in all species
(see http://www.ensembl.org/Multi/newsview?rel=40 for more detail)


API changes (all species)
--------------------------

* Updates to reflect schema changes (including setting xref versions  to 0 if undefined, and supporting ditag
tables).

* Support for ODBC database connections


Compara updates (all species)
------------------------------

Protein/Protein: Updates to orthologues/paralogues and families to include the new species and gene sets

Dna/Dna
    * human/macaque blastz (import from UCSC)
    * MLAGAN primate group (human, chimp, macaque)
    * human/opposum blastz net
    * fugu/tetraodon blastz net
    * 2x genomes (elephant, armadillo, rabbit, tenrec) blastz
      against human
    * Drosophila/Anopheles tBLAT
    * Drosophila/Aedes tBLAT
    * Anopheles/Aedes tBLAT


Web features
------------

* New orthologue display - GeneTreeView (all species)
  Displays gene orthologies as tree diagrams (reached from GeneView  by selecting "Gene tree info" from the
lefthand menu bar).

* OMIM (disease) displays (Homo sapiens)
  FeatureView can be configured to display OMIM xrefs and their associated genes.


Schema changes (all species)
----------------------------
Patches have been made including 2 new tables added to support ditags



For more detail see:
http://www.ensembl.org/Multi/newsview?rel=40

Ensembl Webteam