Hi,
The new Ensembl marts for release 57 are now live on www.ensembl.org and
www.biomart.org. The following improvements and modifications have been
made:
Release 57 Ensembl marts (all species)
Ensembl Genes 57
Addition of new species Meleagris gallopavo (Turkey)
Elephant new assembly (loxAfr3), Gorilla new assembly (gorGor3),
Rabbit new assembly (oryCun2.0)
Addition of ortholog ancestor attribute and paralogy type attribute in
the Homologs attribute section
Addition of GO Term Name (e.g. regulation of biological process)
filter as well as GO Term Accession (e.g. GO:0050789) in the GENE
ONTOLOGY filter section
GPCR db filters and attributes removed for Drosophila, as these will
also be removed from Flybase.
The variation filter->variation type is now multi select
Example ID's added to ID list limit filter drop down
Recommended Pubmed ID for the Transcript Event has been added to the
filters and attribute section
Transcript splicing event information added for more species:
- human
- mouse
- rat
- worm
- zebrafish
- fruitfly
Gorilla now has a chromosome drop down in the region filter section
SMART ID URl link has been fixed
Ensembl variation 57
*NEW* Homo sapiens Structural Variation dataset now available
New Horse variation database (dbSNP 130)
New Pig variation database (dbSNP 128)
Update of Rat, Zebrafish and Cow to dbSNP 130
GENE ASSOCIATED VARIATION FILTERS->Consequence Type now multi select
Addition of phenotype drop-down in the variation mart filters
Biomart code has been patched to fix the problem of downstream
sequences missing 1bp for cases where there is an Indel [-/N]
Variation->SEQUENCE VARIATION attribute section now has Strain SNP and
Strain - Other Variants (Indels, Multiple Nucleotide Polymorphisms).
New Variation->variation set information (filters and attributes) in
Human dataset
Restructuring of the strain polymorphism section for mouse and rat and
removal of this radio button for all other species as the genotype
information will now be in the variation attribute section.
Ensembl Functional Genomics 57
Addition of link to Ensembl eFG documentation in filter sections.
Regards
Rhoda
Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
