Tag Archives: annotations


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

UniProt is one of the core resources that provides tremendously important curated information about proteins. You will find links to UniProt in lots of other tools and databases as well, but we’ve always championed going directly there for the full look at all the wide range of information they offer. Their foundation remains solid, but they also continue to add new and useful features over time. Recently they had a webinar to describe some of the new things, and the recording of that webinar will be this week’s Video Tip fo the Week.

The video starts with an overview of the whole UniProt site. The core of their great resource is the same, of course. UniProtKB, UniRef, and UniParc are there for various ways to look across the data. The handy Proteomes collection of the proteins in a given species is available, and they also have reference proteomes from that access point. There’s a short section in the video that’s a guide to the basic search functions.

About 9 minutes in they introduce the UniRule annotation features. When certain conditions are met, an annotation gets applied to a protein–which you can trace from the protein pages by clicking on the UniRule link for that annotation. unirule_sampleAnd their software offers a very cool way to look and see how/when conditions are applied. It will load a decision flow path and highlights what the logic rules were used in that particular case, so you can trace it and understand how a protein got a given item. That’s what I illustrate in the screen shot here.

About 14 min, the topic changed to the new Genome Annotation Tracks. They now offer you a way to take their annotations for a UniProtKB entry and use them with a separate genome browser. They hand you BED or BigBed files for different features. You can also load the whole thing as a Hub file to see all the sequence feature data at once. They are species-specific, and started with human, but others are coming. You can access them from the “Downloads” area of the homepage. The 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 UniProt, check out these new options for additional ways to interact with the high-quality information they provide. Good stuff.

Quick links:

UniProt: http://www.uniprot.org/


The UniProt Consortium (2014). UniProt: a hub for protein information Nucleic Acids Research, 43 (D1) DOI: 10.1093/nar/gku989

Video Tip of the Week: Track Hubs in UCSC Genome Browser

Today’s tip of the week introduces a new feature at the UCSC Genome Browser which we will be adding to our UCSC Genome Browser and UCSC Table Browser tutorials (both free) soon: Track Hubs. Track Hubs are annotation tracks for very large datasets housed at non-UCSC servers that might not be conducive for the custom track utility to manage.

Research groups will be able to create their own track hubs of large datasets for search and viewing. They can also register their tracks hubs with UCSC so that they may be used by the public. Users of the genome browser will be able to load those annotation tracks to the genome and table browsers for viewing and searching. The user guide for viewing, creating and registering track hubs is here.d

Today’s tip takes you on a quick tour to show you how to load and view track hubs using one of the two currently available ones from Washington University of epigenomics data.

Now, as a user, if you don’t find the data you need in the native tracks at UCSC, you have two additional places to look, the custom tracks shared by many users here and the track hubs of larger datasets.