Viewing Ensembl Regulation & ENCODE Using the Matrix

submitted by: gspudich
This tutorial demonstrates how to view sequences potentially involved in gene regulation. These sequences are analysed by Ensembl Regulation based mostly on ENCODE data, along with Roadmap Epigenomics data for human. The end of this tutorial shows how to add the full ENCODE data set to a genome display in Ensembl. The Region in Detail in the Ensembl browser will be explored. You may be interested in: Ensembl Regulation docs: http://www.ensembl.org/info/docs/func ... Region in Detail...

Looking at the Region of the LCT Gene

submitted by: gspudich
A comprehensive overview of how to use the Ensembl Region in Detail view (our main Location view) in order to view data about a genomic region. We focus on the region of the LCT gene in human. Links from this video: Video: Patches and Haplotypes in the Human Genome ( http://youtu.be/sPE9j_Hw9HU ) Video: Browsing RNA-Seq Data in Ensembl ( http://youtu.be/9NUibgdkTRY ) FAQ: What styles are available for the data tracks in views like Region in Detail?(...

Tip of the Week: Visualizing Galaxy

submitted by: OpenHelix

A tip of the week introducing visualizing genomic data using Galaxy's visualization tool. For more information, check out the blog post at http://blog.openhelix.eu/?p=12439

Demo: Using BLAST/BLAT in Ensembl

submitted by: gspudich

We demonstrate the BLAST/BLAT tool in Ensembl. Search for a sequence in www.ensembl.org, and identify hits to the genome, or to genes, with this tool.

Demo: Structural variation for a region

submitted by: gspudich

Large structural variations like CNVs (copy number variation) are explored for a region of the human genome. We use the Ensembl genome browser at www.ensembl.org

Demo: Variation for the ZAP70 gene with Ensembl

submitted by: gspudich

We use the Ensembl genome browser at www.ensembl.org to view small scale sequence variants such as SNPs (single nucleotide polymorphims) along with larger structural variations like CNVs (copy number variation) for the human ZAP70 gene.

Ensembl Overview (given at ErasmusMC, Sept 2011)

submitted by: gspudich

This is an overview of the data available in the Ensembl Genome Browser with a focus on the gene set and sequence variation. Four demos follow this presentation, using www.ensembl.org.

Video tip of the week: Variation Data from Ensembl

submitted by: OpenHelix

For more information about this resource see our blog post at URL http://blog.openhelix.eu/?p=10091. In today's tip I am going redo a movie originally done by Ensembl on SNP information in Ensembl, but I will use the updated Ensembl release 64.

The ELIXIR Database Provider Survey

submitted by: cdsouthan

How biological databases are used in the European Union.

Source Organism and Molecule Information at INSDC and the Trace Archives

submitted by: dougramsey
Guy Cochrane, European Nucleotide Archive, EMBL-European Bioinformatics Institute, Welcome Trust Genome Campus The databases of the International Nucleotide Sequence Database Collaboration (INSDC, DDBJ/EMBL/GenBank) and of the Trace and Short Read Archive collaborations between the NCBI and the EBI provide free and comprehensive access to nucleotide sequencing information, from raw sequencing machine output through to functional annotation. As well as offering a direct public portal into...