Tag Archives: genome browsers

Tip of the Week: one iPad app to rule them all

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There is none.

Ok, so that is the simple answer. The complicated answer is this: my ideal genome browser iPad app would have the flexibility to go from a mass market browser to look at an individual’s genomic variants in a genomic context with information about the research, genes, etc presented in such a manner so that any thoughtful person or doctor could understand, to a full fledged UCSC genome browser type research tool.

So, that’s not feasible. Instead, I’m going to look at three genome browsers for the iPad, two for research, one for the mass market. The former are GeneWall by Bioskoop and Wowser by the Children’s Hospital of Philadelphia, the latter is MyGenome by Illumina (links take you to iTunes app store).

The iPad and other touch tablets are perfect research assistants and the day is fast approaching, if it’s not already here, where most researchers will have one on the lab bench for entering and accessing data.

So what am I looking for in a iPad genome browser?
Navigable: it should have a very intuitive, iPad native navigation. I should be able to pinch and swipe my way through the genome with finely controlled ease.
Comprehensive: I should be able to access my genome of choice, past assemblies, and a huge range of annotations.
Flexible: I should be able to upload my own annotations with ease.

Why not just go to the UCSC Genome Browser? You could, but it fails the first test. It’s definitely usable, but many features available on a computer are not available on the iPad and navigation is obviously not iPad native.

20120509-091620.jpgGeneWall works nicely on the first criteria, but zooming in and out takes several (sometimes many) pinches of the fingers. There is no simple way to zoom in and out or walk the chromosome in a more fine tuned manner. On the second, though it comes with a single genome (human) with only a few annotation tracks so it’s not very comprehensive to start, you can easily add annotation tracks downloaded as bed files. So it has some flexibility. The pathway search and gene list function are nice too. A quick YouTube intro here.

20120509-091959.jpgWowser is somewhat different in that it is an iPad interface to the UCSC Genome Browser. It works natively with the iPad and so is easy to navigate. Zooming and walking was intuitive. On a few different wireless networks it was slow to load, but not excruciatingly so. It is quite comprehensive, including the latest human reference sequence and many, but not all, of the UCSC tracks. The tracks are simple to hide or add in. Future updates are said to be including other genomes and more tracks. I could not find a way to add your own custom tracks or data, so on flexibility GeneWall wins out.

Both apps are great, if not quite “there” yet. I think either would be useful if you are looking at the human genome for research.

20120509-092126.jpgMyGenome is a different beast. From Illumina, it’s audience is not the researcher but the medical professional and patient. It’s a beautiful app with a nice interface. Easily navigable, it was simple to get to the information wanted. There is a lot of information there, but it is still quite limited. I took several variations that effect propensity for prostate cancer and other diseases and was unable to find information on them either because the variation is listed but no information, of variation was in an intergenic region which seemingly isn’t included. A user can not yet upload their own data,or other annotations, which is understandable since by Illumina’s own account this is only the beginning. Currently it’s a great educational tool (though I was a hung for more gene information), in the future it will be a good way to browse your own data.

So the bottom line for all three of these are that they are useful as they stand and for their stated purpose, but I’m looking forward to the future of browsing genome data like I was on an Avatar set :). It’s coming.

Saving your genome views: Ensembl (and UCSC Genome Browser, others)

In the latest update of Ensembl, the developers added the ability to save configurations. This allows you to set your  track views and analysis to a specific configuration and load that configuration at a later time. The blog post linked previously (or here) explains the steps to creating your own configurations you can save and return to. In the future they will be adding the ability to share your configurations with colleagues and other researchers.

UCSC has a similar function they call sessions. You can read more about it here on our blog or go to the sessions user guide at UCSC.

As far as I know, NCBI’s Map Viewer does not have the same functionality (please correct me if I’m wrong).

GBrowse has the ability to save sessions, but since it is an open-source program, it will depend on the specific installation on whether that function is available.

Friday SNPets

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…

Can you spare a genome browser?

Recently I’ve been coming across more and more requests and need for genome annotation and visualization software. Genomes are being completed left and right and researchers need ways to browse and annotate these genomes. There are a lot of tools out there. This post is a quick attempt to start listing those. It is not exhaustive right now, right now there are the ones off the top of my head and those focused a bit on visualization (though there is annotation). I plan to expand this list (have any to suggest) and enhance it with more descriptions as time goes forward. Probably make it a page if it becomes useful enough. I’m not listing databases (such as UCSC Genome Browser, RGD, Ensembl, Flybase, but rather software that researchers can use to create such browsable genomes). So, here we go…

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Got a genome? Need a browser?

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From the GBrowse mailing list the other day came notice of a new way to use GBrowse–without programming! A team from Indiana University has lowered the barrier of entry for anyone with a genome they want to display.  They have created an interface and web server for GBrowse that lets you simply upload your data and make some choices for the display…and voilà!  You have a genome browser. It is called WebGBrowse, and I think it is tremendously helpful.  http://webgbrowse.cgb.indiana.edu

As we push forward with more and more sequence data for anyone’s favorite species, and with personal genomes, a rapid and programming-lite option for examining this data needs to exist.  This is a step in that direction.  All you need to do is get your data into GFF3 format (and they give you a sample), you upload it, you pick some display features, and you can be looking at your genome and annotation features in no time at all.

Even if you decide you wanted to build the standard GBrowse version it would be really helpful for the team to mock it up in the WebGBrowse interface to discuss the features.  It might also be an nice way to get students thinking about such displays and then take them over to the regular GBrowse tools.  I could also see creating displays for your gene of interest with various features that are important for your work, or to display for presentations and papers.  I wonder if there is a lower size limit to what you can display…hmm….

I used their sample file to upload and examine and it was very neat and dramatically quick.  I’m going to try to edit that GFF with some sample data that I’ll pull out of NCBI–just to try it out.  One thing that would make my life just that much easier would be to use the GFF file as a web form so I could just load data in that way.  I can see the need for uploading some things (like lists of genes or primers or variations) and I would want a way to save the output for re-upping and sharing, but I would love to be able to handle each of those separately instead of one big GFF.   Another handy feature would be to be able to load a GenBank format file right up.  I wonder if there is a web converter out there for that (I know it exists on the programming side)…I’ll have to look. Or let me know in the comments if you have one. But these are minor enhancement requests–it seems to work great already.  And maybe I’ll learn more as I spend a bit more time with it.

If you are totally new to GBrowse you might want to have a look at our free tutorial on it. Dozens of research groups are using GBrowse to display their data now, and more are coming along all the time.  It will help you to understand the structure and the kinds of things you can expect–and envision what you want to display.

Anyway–congrats to the team that created WebGBrowse.  I think it will be really useful in many ways.  And it is lifting the burden for biologists that don’t have programming resources–that is seriously helpful.

More like this, please :)

ResearchBlogging.orgPodicheti, R., Gollapudi, R., & Dong, Q. (2009). WebGBrowse – a web server for GBrowse Bioinformatics DOI: 10.1093/bioinformatics/btp239