Tag Archives: ensembl

NAR database issue (always a treasure trove)

The advance access release of most of the  NAR database issue articles is out. As usual, this this database issue includes a wealth of new and updated data repositories and analysis tools. We’ll be writing up additional more extensive blog posts on it and doing some tips of the week over the next couple months, but I thought I’d highlight the issue and some of the reports:

There are a lot of updates to many of the databases we know and love (links to go full text article): UCSC Genome Browser, Ensembl, UniProt, MINT, SMART, WormBase, Gene Ontology,  ENCODE, KEGG, UCSC Archaeal Browser, IMG/M, DBTSS, InterPro and others (we have tutorials on all those listed here).

And, as an indication of the explosion of data available (itself a subject of a database issue article, SRA), there are a lot of new(ish) databases on specific datatypes such as MINAS, a database of metal ions in nucleic acids (nice name :D); doRiNA, a database of RNA interactions in post-transcriptional regulation; BitterDB, a database of bitter compounds and well over 100 more.

And I’ll give a special shout out to my former PI at EMBL because I can, Peer Bork’s group has 4 databases listed in the issue: eggNOG, SMART, STITCH and OGEE. (and he and a couple members are on the InterPro paper also).

This is going to be a wealth of information to wade through!

UCSC Genome Browser: http://genome.ucsc.edu
Ensembl: http://www.ensembl.org/
UniProt: http://www.uniprot.org/
MINT: http://mint.bio.uniroma2.it/mint/
SMART: http://smart.embl.de/
WormBase: http://www.wormbase.org/
Gene Ontology: http://www.geneontology.org/
ENCODE: http://genome.ucsc.edu/ENCODE/
KEGG: http://www.kegg.jp
UCSC Archaeal Brower: http://archaea.ucsc.edu/
IMG: http://img.jgi.doe.gov/cgi-bin/w/main.cgi
DBTSS: http://dbtss.hgc.jp/
InterPro: http://www.ebi.ac.uk/interpro




Video Tip of the Week: Variation Data from Ensembl

Trey introduced me to this “decent collection of video tutorials ” from Ensembl, but he and Mary are currently in Morocco teaching a 3-day bioinformatics workshop & then attending the conference (yes, I am envious!). I am therefore creating this week’s tip based on the tutorials that Trey pointed me to. In today’s tip I am going to parallel a tutorial available from Ensembl on SNP information in order to both: 1) show you haw you can access variation information from Ensembl and 2) compare doing these steps using Ensembl 64 (here in this video) and using Ensembl 54 (archived) (in the Ensembl video).

Bioscience resources often are continuously being developed and improved & it can be difficult to keep videos and documentation up-to-date. That’s why here at OpenHelix we work continuously to keeping our materials up-to-date, with weekly tips on new features and updated tutorials as updated sites become stable.

The Ensembl video (SNPs and other Variations – 1 of 2) is quite nice & provides more detail about the actual Ensembl data than I can in my short movie, but it was done a few years ago on an older version of Ensembl. Since then the resource has been updated, and gone through several new versions of the data. I’m going to follow the same steps that are done in part one of the Ensembl SNP tutorial so that you can see examples of what’s changed & what is pretty much the same. I’d suggest you watch both videos back-to-back to get a good idea of what’s changed, and what types of variation information are available from Ensembl. From that basis I’m sure you’ll be able to watch Ensembl’s second SNP video & apply it to using the current version of Ensembl without much trouble. For more details you can refer to the most recent Ensembl paper in the NAR database  issue, which describes not just variation information but Ensembl as a whole.

Quick links:

Ensembl Browser: http://www.ensembl.org/index.html

Legacy Ensembl Browser (release 54): http://may2009.archive.ensembl.org/index.html

Ensembl tutorial, part 1 of 2: http://useast.ensembl.org/Help/Movie?id=208

Ensembl tutorial, part 1 of 2: http://useast.ensembl.org/Help/Movie?id=211

OpenHelix Ensembl tutorial materials: http://www.openhelix.eu/cgi/tutorialInfo.cgi?id=95

Ensembl Tutorial List: http://useast.ensembl.org/common/Help/Movie?db=core

Flicek, P., Aken, B., Ballester, B., Beal, K., Bragin, E., Brent, S., Chen, Y., Clapham, P., Coates, G., Fairley, S., Fitzgerald, S., Fernandez-Banet, J., Gordon, L., Graf, S., Haider, S., Hammond, M., Howe, K., Jenkinson, A., Johnson, N., Kahari, A., Keefe, D., Keenan, S., Kinsella, R., Kokocinski, F., Koscielny, G., Kulesha, E., Lawson, D., Longden, I., Massingham, T., McLaren, W., Megy, K., Overduin, B., Pritchard, B., Rios, D., Ruffier, M., Schuster, M., Slater, G., Smedley, D., Spudich, G., Tang, Y., Trevanion, S., Vilella, A., Vogel, J., White, S., Wilder, S., Zadissa, A., Birney, E., Cunningham, F., Dunham, I., Durbin, R., Fernandez-Suarez, X., Herrero, J., Hubbard, T., Parker, A., Proctor, G., Smith, J., & Searle, S. (2009). Ensembl’s 10th year Nucleic Acids Research, 38 (Database) DOI: 10.1093/nar/gkp972

Customization of views at Ensembl

Hi folks–we’re on the road doing workshops this week, back to near our old stomping grounds of upstate New York, in fact! So I won’t be able to write blog posts. Luckily Ewan Birney of Ensembl published one over the weekend that you should check out. In it he describes some of the newer features in Ensembl that will help you to group and show features in the human genome browser that you might be interested in. Check out his post:

Customising Ensembl Displays

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Tip of the week: CompaGB for comparing genome browser software

Here at OpenHelix we think a lot about the differences between nominally similar software that will accomplish some given task.  For example, in our workshops we are often asked about the differences between genome browsers.  Although UCSC sponsors our workshops and training materials on their browser, we know they aren’t the only genome browser out there and we can talk about them all–in fact, that’s one of the coolest things about being separate from UCSC or a specific software tool provider/grant–we can talk about everyone! And our answer is usually something like this:

The basic foundation of the “official reference sequence” is usually the same in all the main browsers. However, the way they choose to organize the display, the tools for showing/hiding annotation data, and the custom query and display options vary. But they generally all have some mechanism for this. For me, usually the choice comes down to what data I need to look at–and how a given software tools shows me that and lets me interact with it.

I know that’s largely an end-user perspective, but that’s who is attending our workshops. I can remember talking to one guy at our conference booth who only wanted to use a genome browser with the reference sequence display organized vertically. I gave him Map Viewer. Some people need a specific species–and no matter how good the software is, if your research species isn’t in there, it just doesn’t matter…. I’ve seen super-users on twitter complain about the look of the background at one browser or another. That doesn’t have much bearing on my choice–but I do have to say I really hate “hidden” menus and features you have to hover and dig to find, in general. What you don’t see is just impossible to know as an end-user.

But quite frankly when I’m looking for some details in a given region for a research use, I often explore all the browsers I know because of their differences in display and available data to show–to make sure I’m not missing anything. It doesn’t take that long to use them all (if you know your way around, and I think I do…).

But one group has tried to quantify the differences between software tools in a standardized way with with specific metrics. A group from INRA has collected and assessed various characteristics of genome browsers, and has developed a database where you can look at what they have curated. It’s called CompaGB.

You can assess the features as one of these profiles: biologist, computational biologist, or computer scientist at this time.  In this tip of the week I explore the CompaGB interface, from an end-user biologist perspective. I’ll choose a couple of browsers to compare, and we can look at the type of things that the CompaGB team scores to give you a sense of what you can find. For developers you’ll see there are different metrics and you should go back and explore those as well.

In their paper they describe their inspiration for this project–which is QSOS. The Qualification and Selection of Open Sources software project provides a model and framework to standardize descriptions of available software features. The QSOS framework is illustrated in this graphic on their Welcome page:

In short, they have 4 steps: defining frames of reference appropriate for the software tool; assessing the features; qualify the features with a weighting mechanism, and selecting the appropriate tool.

You can easily see how the CompaGB team integrated these ideas in their database of genome browser comparisons. They let you choose criteria you are interested in, and offer a radar plot display as well as a tabular representation of the scores so you can consider the overall view or the details.

There are scores for “full, limited/medium, and poor” but not a lot of detail on that. They assessed the tools in 4 sections: (1) technical features, (2) data content, (3) GUI, and (4) annotation editing and creation.  There is apparently no swimsuit competition. Alas.

The paper says that 4 different evaluators examined the tools (at this time 7 different genome browser: MuGeN, GBrowse, UCSC, Ensembl, Artemis, JBrowse, Dalliance). They have version numbers–for example you can compare the 2 widely used GBrowse versions right now. How often these will get re-evaluated I don’t know. And how to compare different installations of GBrowse at different sites is not really clear to me–they can vary a lot by what the project team wants and needs to implement.

One evaluator did each tool in most cases. And reportedly the results were sent to the database providers for checking. I have no idea what was sent to UCSC on the training issue… [*cough* I have issues with the UCSC training score details, for example...Yeah, we do workshops and so does UCSC. Lots of workshops around the world, we have slides and exercises...I'll show you in the tip where I saw it.] They do encourage users to comment or suggest on their web site if you have supplementary information–I may want to add some details later ;)  And it appears possible to create new items and curate, but I haven’t tried this. They also say they are re-vamping the evaluation process going forward to simplify it.

But…this statement in their paper surprised me:

The UCSC browser natively displays a broad range of human annotations, including cross-species comparisons. UCSC browser’s underlying strategy focuses upon centralizing data on UCSC servers and, as far as we know, no external lab has installed it locally for the purpose of storing and browsing their own data.

Ummm–no. We talk to people all over the place who maintain local installations of UCSC. Quite often in hospital situations where patient data privacy is a major issue there are local installs; certain companies have them. But there are others as well–among them a bunch of mirrors around the world. There’s a whole separate mailing list where people discuss their issues with their own installations. But we’ve also seen the UCSC infrastructure used for other species that UCSC doesn’t support such as HIV, malaria, phage browsers, and more.  Maybe this unusual setup of the UCSC software at the Epigenetics Visualization Hub would be interesting to be aware of. And we know the UCSC team consults with groups and helps them to do it.  And by the way–we mention in our tutorials and workshops that we’ve done around the world that other installations are possible and available.  And we know that the materials we provide are used in many countries to do local trainings as well.

So it was an interesting attempt to measure software features, and I understand why they attempted it, but it seems challenging to scale and maintain. And the curation strategy will have to be considered when evaluating the data. These are fixable if the project proceeds beyond this early set of browsers and branches out to other types of open source software. It really is hard to know what’s worth spending your time on, I admit. And that’s why we hope end-users have a look at our training materials to get introduced to a specific site and see if it suits their needs, and they can kick the tires with the exercises.


Quick links

CompaGB: http://genome.jouy.inra.fr/CompaGB/

QSOS: http://www.qsos.org/


Lacroix, T., Loux, V., Gendrault, A., Gibrat, J., & Chiapello, H. (2011). CompaGB: An open framework for genome browsers comparison BMC Research Notes, 4 (1) DOI: 10.1186/1756-0500-4-133

Naked Mole Rat, another day, another genome

The latest genome to be completed is the naked mole rat (Heterocephalus glaber). Now, could there be a cooler (if ugly) mammal on the planet? It’s one of only two truly eusocial mammals in the world, it lives up to 28 long years (my daughter’s rat, no relation, lived only 3 years) and is surprisingly resistant to a lot of diseases.

So, no wonder the genome was sequenced. Maybe we can learn some things about social behavior and longevity.

Of course there is a resource for it at http://www.naked-mole-rat.org/ though it’s basically just a blast server and some downloads. I’m counting down to the day it’s available at UCSC or Ensembl :D. I have some genes I’m interested in comparing.

Alternate sequences in UCSC and Ensembl

If you go to the UCSC Genome Browser and type “vars” in the “gene” text box (human genome, 2009 assembly), you’ll notice something different. The chromosome region listed is “chr6_apd_hap1:3,060,047-3,078,462″  Those are the haplotype sequence coordinates. With the addition of the hg19 assembly, now provided by GRC, additional alternative sequences were included: haplotypes, alternative loci and patches.

Now type in “vars” in the “position or search term” box, or “chr6:30,000,000-31,000,000″ and submit.

Now to go the Mapping and Sequencing tracks and change the “GRC Patch Release” Menu to “pack.” Click the title link and you’ll see you can turn on either the haplotypes or the patch releases.

Once you do that, click refresh.

Here you will be able to see all those alternative sequences provided by the GRC.

It will look something like the the screenshot below.



Click on any of the sequence icons and get more information about that sequence. You can read more about the GRC haplotype and patch release at the site.

The Ensembl browser too of course has these alternative sequences included. Instead of going through how to access them here, I’ll point you to their very informative blog post on that very subject.




Workshop: World Tour of Genome Browser and Galaxy of Analysis Tools

Would like to just announce that Mary and I will be giving an all-day hands-on workshop on Tuesday, November 2nd, 2010 in Washington DC (my home town), right before the ASHG conference (where we will also be). The title of the workshop is A World Tour of Genome Browsers and a Galaxy of Analysis Tools. We’ll be covering UCSC Genome and Table Browsers, an overview of other genome browsers, BioMart, Galaxy and a tour of genome resources and how to find them. For more information on location, cost, topics you can continue reading here. There are workshops on UCSC and Galaxy at ASHG  for attendess (which we will be at, but Bob, Anton and others will be doing), but those have sold out and filled up. We are offering this workshop for those who would like to learn these topics and more, both DC residents and ASHG attendees.

To purchase a seat and register, go to our upcoming workshops page.

Continue reading

Friday SNPpets

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

Tip of the Week: 1000 Genomes Project Browser

You may have been hearing about the 1000 Genomes project–it’s one of the ongoing “big data” projects that is going to yield a great deal of variation information about the human genome. The goal is to sequence well over1000 genomes to identify “most genetic variants that have frequencies of at least 1% in the populations studied”.  They are doing this by sequencing large numbers of samples  with 4x coverage. You can read more about their strategy in their About page on their web site. It also lists the anticipated sample populations.

In this week’s Tip of the Week I’m going to take a quick spin through their browser. (You can also download all the data, but I’ll be focusing on the browser.) They have begun to release data now, and there are 6 individual sequences available at this time.  These are part of their “pilot” studies.  You can get some details on the pilot from their about page, which links to this PDF about the samples.

They are using the Ensembl framework to display their data. So if you are familiar with using Ensembl you’ll have some facility moving around this browser.  One thing that isn’t apparent right away from the site is that you can click the Resembl link on the display to turn on a track that puts the read/coverage data on the viewer. I also liked the alignment display  of all 6 genomes–but I’m sure that’s going to get challenging to view later with more and more genomes.

In an exchange with their very helpful help desk yesterday, I got this quick summary of the samples you’ll see:

For the high coverage populations NA12891, NA12892 and NA12878 are the CEU trio, NA19238, NA19239 and NA19240 are the YRI trio both father, mother, child respectively and both children were daughters.

If you have questions about their data, be sure to go ask them for help–they were very speedy with answers for me :) .

Some of the project data has also been picked up by UCSC and you can access the same sequences in the UCSC Genome Browser in the Genome Variants track on the March 2006 human assembly. (You’ll also see Venter, Watson, and some other individual genomes there).

Quick links:

The Project: http://www.1000genomes.org/

The Browser: http://browser.1000genomes.org/

An article in Science with some background:  A Plan to Capture Human Diversity in 1000 Genomes