Question: Useful information about Ensembl release 63 mart databases
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gravatar for Rhoda Kinsella
7.9 years ago by
Rhoda Kinsella660 wrote:
Hi, The new Ensembl marts for release 63 are live on www.ensembl.org and www.biomart.org. The following improvements and modifications have been made: Ensembl Genes 63: Updated to new Microbat assembly Myoluc2.0 Updated to new Yeast assembly EF3 Added a new Exon ID filter to the GENE->Limit to genes filter. Reinstated the protein allele attribute in the Variation->GERMLINE VARIATION INFORMATION attribute section. The PRIDE team have collaborated with us to reinstate the linking between the Ensembl Gene mart and the PRIDE mart. The Exon ID was removed from the Transcript Event attribute section as this was misleading. The text (bp) was removed from the GO attributes. Gene and transcript biotype attributes have been added to the Sequence attribute section. The HGNC symbol link has been updated. The following external references are now stored on gene IDs: EntrezGene, WikiGene, RFAM, MIM, MIM_GENE, MIM_MORBID, miRBase, UniGene, Uniprot_genename, DBASS3, DBASS5 Ensembl Variation 63: Updated mouse to dbSNP 132 Phenotypes in the GENERAL VARIATION FILTERS->Phenotype filter drop down have had all commas removed as this caused problems for the biomart code which resulted in incorrect filtering. Peptide shift attribute has been reinstated in the Variation->GENE ASSOCIATED INFORMATION attribute section. The Variation->SEQUENCE VARIATION->Variation annotation attribute section has been renamed Phenotype annotation Variation ID attribute has been renamed Variation Name Ensembl Regulation 63: "Is projected" attribute added to the Regulatory features. Annotated features have now been renamed to Regulatory Evidence Useful text information on how to use the filters and attributes for this mart has been added to the top of the filter panel and the top of the attribute panel on the interface. Vega 43: Human and Danio manual annotation has been updated to represent the annotation presented in Vega release 43. 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]]
annotation go yeast vega • 588 views
ADD COMMENTlink written 7.9 years ago by Rhoda Kinsella660
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