<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
</head>
<body bgcolor="#ffffff" text="#000000">
Hi,<br>
<br>
Please see below a list of intentions declared for Ensembl release 64
(scheduled for September).<br>
Please not that these are intentions and are not guaranteed to be in
the release.<br>
<br>
<br>
Thanks,<br>
Magali<font face="Courier"><br>
<br>
<br>
<br>
=======================================<br>
Declarations of Intentions - Ensembl 64<br>
=======================================<br>
<br>
<br>
Compara<br>
=======<br>
<br>
Pairwise alignments (All Species)<br>
---------------------------------<br>
~ human vs cow lastz alignments<br>
~ human vs tasmanian devil lastz alignments<br>
~ human haplotype alignments for high coverage blastz-net alignments<br>
~ human vs lamprey tblat alignments<br>
~ lamprey vs Ciona intestinalis tblat alignments<br>
~ lamprey vs Danio rerio tblat alignments<br>
~ lamprey vs Gasterosteus aculeatus tblat alignments<br>
<br>
Multiple alignments (All Species)<br>
---------------------------------<br>
~ 12way-mammal EPO alignments to incorporate new cow<br>
~ 19way-amniota Pecan alignments to incorporate new cow<br>
~ 35way-mammal low-coverage-EPO alignments (new cow)<br>
<br>
Syntenies (All Species)<br>
-----------------------<br>
~ human-cow synteny<br>
<br>
ProteinTrees and homologies (All Species)<br>
-----------------------------------------<br>
GeneTrees (protein-coding) with new/updated genebuilds and assemblies<br>
~ Clustering using hcluster_sg<br>
~ Multiple sequence alignments using MCoffee without the
exon-disaligner module, or Mafft<br>
~ Phylogenetic reconstruction using TreeBeST<br>
~ Homology inference including the recent
'possible_ortholog','putative gene split' and 'contiguous gene split'
exceptions<br>
~ Pairwise gene-based dN/dS scores for high coverage species pairs
only (both on orthologues and paralogues)<br>
~ GeneTree stable ID mapping<br>
<br>
ncRNAtrees and homologies (All Species)<br>
---------------------------------------<br>
~ Classification based on Rfam model<br>
~ Multiple sequence alignments with infernal<br>
~ Phylogenetic reconstruction using RaxML<br>
~ Phylogenetic reconstruction using FastTree2 and RaxML-light for very
big families<br>
~ Additional multiple sequence alignments with Prank (w/ genomic
flanks)<br>
~ Additional phylogenetic reconstruction using PhyML and NJ<br>
~ Phylogenetic tree merging using TreeBeST<br>
~ Homology inference<br>
<br>
Protein Families (All Species)<br>
------------------------------<br>
Updated MCL families including all Ensembl transcript isoforms and
newest Uniprot Metazoa.<br>
~ Clustering by MCL<br>
~ Multiple Sequence Alignments with MAFFT<br>
~ Family stable ID mapping<br>
<br>
Compara dumps (All Species)<br>
---------------------------<br>
~ EMF dumps for 20 way PECAN multiple aligments<br>
~ BED files for 20 way GERP constrained elements<br>
~ EMF dumps for 12 way EPO multiple aligments<br>
~ EMF dumps for 35 way low-coverage alignments<br>
~ BED files for 35 way low-coverage alignments<br>
~ Data dumps for ProteinTrees<br>
~ Data dumps for ncRNAtrees<br>
<br>
API/schema changes (All Species)<br>
--------------------------------<br>
~ changes in the class hierarchy (NestedSet-Member-AlignedMember) to
achieve better flexibility and fight code redundancy<br>
~ possible changes in the schema: adding a new "header" table for a
tree root, moving general properties of the tree into that table<br>
~ possible changes in the schema: adding tables for tree's properties
and node's properties to make tag storage and extraction more efficient<br>
<br>
<br>
Core<br>
====<br>
<br>
Xref projections (All Species)<br>
------------------------------<br>
Project GO IDs and gene names to species.<br>
<br>
Xrefs (All Species)<br>
-------------------<br>
Update xrefs for human, mouse, sea squirt ciona intestinalis and ciona
savignyi, madagascar hedgehog, western european hedgehog, mouse lemur,
platypus, bushbaby, shrew, squirrel<br>
<br>
schema change (All Species)<br>
---------------------------<br>
is_ref will be added to the alt_allele table to show which is the
reference gene.<br>
<br>
Embl/ Genbank flat file dumps (All Species)<br>
-------------------------------------------<br>
<br>
Schema version update (All Species)<br>
-----------------------------------<br>
patch_63_64_a.sql<br>
update schema version to 64<br>
<br>
LRG import (Human)<br>
------------------<br>
Import of new LRG sequences<br>
<br>
<br>
Funcgen<br>
=======<br>
<br>
New Regulatory Data (Human and Mouse)<br>
-------------------------------------<br>
~ New Mouse MEL cell-line regulatory build, including Dnase-Seq, and
ChIP-Seq for p300, cMyb, USF2, Rad21, NELFe and Max. All data is from
ENCODE, following their data policies.<br>
~ New Human CD4 ChIP-Seq data for CBP, p300, MOF, PCAF, Tip60, HDAC1,
HDAC2, HDAC3 and HDAC6 (Wang et al, 2009). A new regulatory build was
made to incorporate this data.<br>
<br>
MotifFeatures: Scores Rounded (All Species)<br>
-------------------------------------------<br>
MotifFeature scores were rounded to 3 decimal places.<br>
<br>
MicroArray Mapping (Human, Mouse and Rat)<br>
-----------------------------------------<br>
Micro array mapping has been performed for those species with new
assemblies or updated gene builds.<br>
<br>
DNA methylation DAS tracks (Human)<br>
----------------------------------<br>
We have updated the set of DNA methylation DAS tracks using data
available from the ENCODE project.<br>
<br>
patch_63_64_a - Schema version (All Species)<br>
--------------------------------------------<br>
The schema_cersion entry in the meta table has been patched to version
64.<br>
<br>
patch_63_64_b - Cell type experimental factor ontology ID (All Species)<br>
-----------------------------------------------------------------------<br>
The cell_type table has had an efo_id field added to represent links to
the Experimental Factor Ontology.<br>
<br>
patch_63_64_c - Experimental meta data (All Species)<br>
----------------------------------------------------<br>
A patch has been applied to add fields to capture experimental meta
data e.g. archive & pubmed IDs<br>
<br>
<br>
Genebuild<br>
=========<br>
<br>
Lamprey genome (Lamprey)<br>
------------------------<br>
A full annotated gene set for the lamprey genome<br>
<br>
Human cDNA update (Human)<br>
-------------------------<br>
New cDNA db for human.<br>
<br>
GRCh37.p5 (Human)<br>
-----------------<br>
Adding the fifth patch release for the human assembly. This alters the
assembly information in all human databases.<br>
<br>
GRCh37.p5 annotation (Human)<br>
----------------------------<br>
Annotation of the patches in the other features db, including
projection of annotation from the primary assembly.<br>
<br>
Cow genebuild (Cow)<br>
-------------------<br>
A new genebuild has been done on the cow UMD 3.1 assembly.<br>
A new otherfeatures database has also been prepared.<br>
<br>
Mouse gene set update (Mouse)<br>
-----------------------------<br>
The merged gene set has been updated to incorporate the latest Vega
manual annotation.<br>
<br>
Tasmanian Devil Genome (Tasmanian devil)<br>
----------------------------------------<br>
A genebuild on the Tasmanian Devil 7.0 assembly has been created along
with an otherfeatures database containing RNASeq models.<br>
<br>
Update to Ensembl-Havana GENCODE gene set (release 9) (Human)<br>
-------------------------------------------------------------<br>
Update to Ensembl-Havana GENCODE gene set (release 9) based on Ensembl
gene set and latest Havana gene annotation.<br>
<br>
GENCODE RNA-Seq (Human)<br>
-----------------------<br>
<br>
Human Vega annotation (Human)<br>
-----------------------------<br>
Manual annotation of human from Havana has been updated. This
represents the annotation presented in Vega release 44. Annotation by
Havana of chromosome 14 has been completed.<br>
<br>
Mouse Vega annotation (Mouse)<br>
-----------------------------<br>
Manual annotation of mouse from Havana has been updated, including
annotation of the MHC region on chromosome 17. The data represents the
annotation presented in Vega release 44.<br>
<br>
Mouse cDNA update (Mouse)<br>
-------------------------<br>
The latest set of cDNAs for mouse (as of dd/mon/yyyy) from the<br>
European Nucleotide Archive and NCBI RefSeq were aligned to the<br>
current genome using Exonerate.There are nnnn new cDNA for Ensembl 64.<br>
<br>
Flagging obsolete Uniprot proteins (All Species)<br>
------------------------------------------------<br>
Flag the obsolete proteins in Uniprot used as supporting evidence<br>
<br>
Flagging obsolete Ensembl proteins (All Species)<br>
------------------------------------------------<br>
Flag obsolete human Ensembl proteins used as supporting evidence<br>
<br>
Gorilla 3.1 projection (Gorilla)<br>
--------------------------------<br>
A new AGP file has been provided for gorilla, using the same contigs
but with different gaps sizes. Genes from the e63 release will be
projected onto the updated assembly.<br>
<br>
Removal of ambiguous bases from Takifugu rubripes (Fugu)<br>
--------------------------------------------------------<br>
Removed the 'R' and 'Y' ambiguous bases from scaffold_20 in
takifugu_rubripes_core_64_4.<br>
<br>
<br>
Mart<br>
====<br>
<br>
Ensembl 64 mart databases (All Species)<br>
---------------------------------------<br>
Full build of all seven marts for release 64<br>
<br>
<br>
Variation<br>
=========<br>
<br>
dbSNP 133 import (Cow)<br>
----------------------<br>
dbSNP Build 133 for cow based on the UMD_3.1 assembly.<br>
<br>
<br>
LRG variant import (Human)<br>
--------------------------<br>
variants on LRG sequences<br>
<br>
Phenotype annotations (Human)<br>
-----------------------------<br>
~ COSMIC import update. Minor changes in COSMIC sample names<br>
~ OMIM, NHGRI GWAS catalog, UniProt and EGA updates<br>
<br>
Schema changes (All Species)<br>
----------------------------<br>
~ Schema changes for structural variations<br>
* Add a structural_variation_feature table: store the coordinates<br>
* Modification of the structural_variation table: remove the
coordinates<br>
~ Additional enum in variation source table for LSDBs<br>
<br>
Web display updates (All Species)<br>
---------------------------------<br>
~ For the variation displays, we will add more detail to the
consequence table, including displays showing the DNA sequence change
and amino acid changes.<br>
~ Add a variation annotation panel in the Gene section<br>
<br>
update consequences for transcript alleles (Human and Mouse)<br>
------------------------------------------------------------<br>
update human and mouse variation transcript alleles due to new gene
builds<br>
<br>
Structural variation (Dog, Human, Mouse and Pig)<br>
------------------------------------------------<br>
~ Update structural variation data from DGVa for Human, Mouse, Dog and
Pig.<br>
~ Add COSMIC structural variation data (Human).<br>
<br>
<br>
</font>
</body>
</html>