unirule_sample

Video Tip of the Week: UniProt updates, now including portable BED files

… video also described a bit about the structure there as well. So you could take these files to ENSEMBL or UCSC Genome Browser and load them, with all the UniProt features now to compare to the existing genomic context at those browsers. They illustrate how you can look at the “active site” annotations, but you can also look at post-translation modification sites, domains, etc. This was a feature that was new to me, and looks like a terrific idea.

So even if you think you know …

View External Tools

Video Tip of the Week: Send UCSC Genome Browser sequence to external tools

… get there.

There are a range of options. You can still jump right to NCBI Map Viewer or Ensembl to look at the same region in their browsers. But now you can select primers, see restriction sites, look at RNA characteristics, find protein domains, or examine CRISPR tools. You can look for transcription start sites or some TF binding motifs. Here’s this week’s Video Tip that shows the process.

You can still “get DNA” if you want to. And you can still use the Table …

Genomics England is responsible for the 100,000 Genomes Project

Video Tip of the Week: PanelApp, from the 100000 Genomes Project

… Home Reference, the Decipher DDD project, HGNC, ClinVar, UniProt, NCBI Nucleotide, and ENSEMBL among others to add phenotype and gene details of many types. So for any gene you can keep digging for addtional information.

There are a long more details over at the announcment post:    New rare disease gene tool launched – PanelApp. But I think the structure and color cues are helpful. (Wait, colour, right? UK variation). Check it out yourself, though, with the link below. You …

ClinGen

Video Tip of the Week: ClinGen, The Clinical Genome Resource

… a genome viewer right on the page.  But you can also choose to look at external browsers at NCBI, Ensembl, or UCSC. I clicked the UCSC Genome Browser one to see how it displayed, and they automatically present to you tracks with the relevant ClinGen data loaded.

In other tips I’ll talk about other pieces of the infrastructure that they are building or coordinating with. Some we’ve talked about before–you can see a previous tip that included the ClinVar resource at NCBI that is …

Video Tips of the Week, Annual Review 2013 (part 2)

… Protein Family Sorter

October 30: VectorEditor

November 2013:

November 6: ENCODE @ Ensembl

November 13: Advanced Topics in GenoCAD

November 20: IGB, Integrated Genome Browser

November 27: Thanksgiving holiday break, but see Thanksgiving Genomes.

December 2013:

December 4:  Creating an Electronic Informed Consent

December 11: UCSC Track Hubs

December 18: CodersCrowd

December 25: Annual Tip Review part 1

VideoTip of the Week: ENCODE @ Ensembl

… @ UCSC ), tips and  information about ENCODE. We also have a lot of tutorials (again 2, Ensembl and Ensembl Legacy - on the older versions ), tips and information about Ensembl, the database and browser at EBI.

Now here is a tip of the week on both Ensembl AND ENCODE. This is one of the more recent additions to Ensembl’s video tutorials. This video looks at how to identify sequences that may be involved in gene regulation. Most of this data at Ensembl is based on …

Video Tips of the Week, Annual Review V part deux

… MaizeGDB Genome Browser & other videos

August 15: Browsing Butterflies with GBrowse and Ensembl

August 22: G-nome Surfer for table-top genome browsing

August 29: GenoCAD for Synthetic Biology

September 2012

September 5: MetaboAnalyst 2.0

September 12: ENCODE enables smaller science

September 19: 3D Virtual Worm (encore)

September 26: 1000 Genomes Dataset Browser from NCBI

October 2012

October 3: JBrowse for genome browsing

October 10: Let …

Video Tip of the Week: Turkeys and their genomes

… your Thanksgiving Dinner, you can check out the UCSC Genome Browser or the Turkey Browser at Ensembl for that. The NCBI turkey genome site also tells us that the karyotype tastes like looks like chicken!

You can also scope out the  Meleagris gallopavo sequencing paper that came out a couple of years back. You’ll be eating 16,000 annotated avian genes.

Reference:

Dalloul, R., Long, J., Zimin, A., Aslam, L., Beal, K., Ann Blomberg, L., Bouffard, P., Burt, D., …

Video Tip of the Week: 1000 Genomes Dataset Browser from NCBI

… the official 1000 Genomes project site, or through the official 1000 Genomes version of the Ensembl Browser. As you might imagine for a “big data” project such as this, data has been added to a variety of NCBI databases, including dbSNP, the Sequence Read Archive (SRA)  and BioSample. Although you could search for this data through the universal Entrez search system, previously to view the data you would have to view individual results at each separate database. The 1000 …

Video Tip of the Week: Browsing Butterflies with GBrowse and Ensembl

… group has a GBrowse at MonarchBase. In addition, the data for both is also now included in Ensembl as of the July 2012 release 15. [note: see administrative details in the comments --mm]

For this week’s tip we fly around from the species-specific GBrowsers to the collected sets at Ensembl. It’s great to have the species-specific sites for depth of information about the projects and resources, but it’s also nice to have the additional tools and displays of the larger genome …