Question: Ensembl mart release 57: Useful information
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gravatar for Rhoda Kinsella
9.0 years ago by
Rhoda Kinsella660 wrote:
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. [[alternative HTML version deleted]]
snp go homo sapiens zebrafish • 673 views
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