Tag Archives: genome browser

Tip of the Week: MycoCosm

MycoCosm is a fungal genomics database and browser at JGI, home of a lot of great resources. This week’s tip is from their video tips, which are useful. MycoCosm includes browsers of annotated data of many fungal genomes, KEGG pathway data, synteny data and much more. Their list of video tips include an introduction to the resource, functional annotation browser and protein page intro. Here is the one to get you started on the browser (unfortunately, there is no embed capability, so the image here will take you to the tutorial). These video tips are longer than our usual 5 minute tips ranging from 6 minutes (intro) to just over 30 (browser).

Cutest genome yet

pandaIn the ongoing series of Another Day, Another Genome….we add the giant panda!  By far the cutest genome yet.  Well, ok, I actually haven’t seen the genome yet as the site was down last night when I tried.  But I’m sure it’s adorable. Her name is Jingjing, and she is a 3 year old panda and was also the 2008 Olympic mascot, according to the supplement info.  She’s a supermodel of pandas, I guess.

Hat tip to James and the Giant Panda Corn

The paper is here:  The sequence and de novo assembly of the giant panda genome

The database and sequence is here: http://panda.genomics.org.cn The browser looks nice, but I’ve found some odd implementations.  The ? tools yields the messsage “this tool is empty”. Got the same message from the Config button.  Documentation a bit sparse. Sigh.  More later as I look harder at it.

Update: The browser implementation threw me at first, reminded me of JBrowse but not exactly. As they describe:

We illustrated the panda genome data in a MapView, which is powered by Google Web Toolkit . A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads.


Tip of the week: JBrowse, a game changer?

jbrowse_tipIn most of software and database development the changes that are coming along all the time seem to be tweaks and polishes on the existing strategies. Every so often, though, there’s a big shift in the strategy or mechanism. This week the JBrowse paper I read made me realize that is now firmly underway. Today’s tip of the week will introduce JBrowse, and here I’ll describe some of the reasons this is a game changer.

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New and Expanded Free Tutorials on UCSC Genome Browser Now Available

University of California, Santa Cruz and OpenHelix announce the free availability of online free tutorial suites on the UCSC Genome Browser.

June 3, 2009 — University of California, Santa Cruz and OpenHelix today announced the free availability of tutorial suites on theUCSC Genome Browser, a powerful and popular freely available web-based tool for mining genomic data. The three tutorial suites now available include a general introduction to the genome browser, an introduction to the Table Browser and custom tracks functions of the Genome Browser, and an introduction to additional tools available, including Gene Sorter and VisiGene.

UCSC Genome Browser is a research tool that integrates the work of hundreds of scientists worldwide into a graphical display of genome sequences and aligned annotations. The Genome Browser — originally developed to assist in the initial assembly of the human genome — now features a rich set of annotations on a multitude of mammalian and model organism genomes.

The tutorial suites, created and maintained by OpenHelix, a provider of training on bioinformatics and genomics resources, include an online, narrated, multi-media tutorial, which runs in just about any browser connected to the web and can be viewed from beginning to end or navigated using chapters and forward and backward sliders. The approximately 60 minute tutorials highlight and explain all the features and functionality needed to start using the Genome Browser and its tools effectively. The tutorial also includes a step-by-step movie which walks the user through an exercise using the tools of the Genome Browser. The tutorial can be used to learn how to use the Genome Browser, to view new features and functionality, or simply as a reference tool to refresh users’ memory.

Also included with each tutorial is a suite of training materials, including PowerPoint slides used as a basis for the tutorial, with a suggested script for the slides, slide handouts, and exercises. These materials can be used as reference for users or as a ready-made presentation for training others on the use of the Genome Browser.

The tutorial suites are used in many ways, including:

  • Researchers use the tutorial suites to learn how to use new or unfamiliar genomics resources they need as their work progresses.
  • Faculty and Staff use the tutorial suites to keep abreast of resources and technology, using the resource as an excellent staff training and career development tool.
  • Faculty uses the tutorial suites to save significant time in creating classroom content and to augment in class learning.
  • Faculty, Staff and Students can use the tutorials as a valuable asset to learn and review how to use these resources at any time.

You can view the UCSC Genome Browser tutorials suites at www.openhelix.com/ucsc.

OpenHelix provides over 70 other tutorial suites on a number of genomic databases and resources through an individual, group, or institutional subscription. Further information can be found at OpenHelix.

About OpenHelix
OpenHelix, LLC, provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

About UCSC Bioinformatics Group
The UCSC Bioinformatics Group is part of the Center for Biomolecular Science and Engineering (CBSE) at the University of California, Santa Cruz. Director and HHMI investigator David Haussler leads a team of scientists, engineers and students in the study and comparative analysis of mammalian and model organism genomes. Research Scientist Jim Kent heads up the engineering team that develops and maintains the UCSC Genome Browser. The UCSC Bioinformatics Group continues to uphold its original mission to provide free, unrestricted public access to genome data on the Web.

Got a genome? Need a browser?


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

How do you represent genomes?

cnv_1Not just the genome, but genomeS. As Jan at Saaien Tist has mentioned, human (and other species) genomes are quiet variable. Though the linear representation of genome browsers makes perfect sense (like the UCSC Genome Browser, Ensembl, GBrowse and MapViewer among others) for much annotated data of the genome, structural variations are not so well visualized in a linear representation. And, as we are find the human and other specie genomes are quite variable, we might need to come up with another way to visualize these genomic data beyond the ‘reference genome’ linear model. Jan suggests deBruijn graphs,
pictured here. I find some difficulty in ‘visualizing’ how these are going to work for the _other_ annotations in the data. Though this representation looks like it might work great for CNV and the like, it seems to make viewing other types of data (expression, SNP, etc) more complicated. I’m looking forward to see how this develops.

Or perhaps we’ll be looking at genomes like this (ok, maybe not, but it’s geeky cool).

Ensembl 51

Ensembl has updated their website to version 51 (long awaited) if you haven’t already noticed. I’ve been doing some preliminary browsing of the new interface and have some first impressions:

* like any change, it’s taking some getting-used to. It’s not a minor change in the navigation or configuration interface.

* The backend does seem to have better performance, pages in the browser and searches do appear to load must faster than I am used to.

* I like that they have added a simpler way to add your own data, though as yet I haven’t found an easily accessible explanation of formatting the data. Admittedly, I’ve only given it a cursory look. I’ll play around with this more.

* As yet, I’m not sure I like the new interface to adding tracks to the display better. I liked the pull-down menus they had before. Easy to find, add and close. Perhaps it’s one of those things you just get used to and find to be better than the older interface after you use it more.

Well, we’ll be poking around a bit more and let you know what we find.

Ensembl Updating

ensembl updateEnsembl has been teasing about an update for a while now, version #51. It’s not out  yet :). But today on the Ensembl blog they do have a bit of a preview. It has a new design, some new stuff under the hood to make it run better, a new configuration panel and some of the tracks will behave differently (more options). They give a screenshot of the new interface, but it’s not particularly large, so you get the gist of it at least. No word other than “the web team are working hard to tidy up the loose ends of the release!,” so we assume that will be soon. Looking forward to it.

Bacterial Browser ala Google Maps

Came across a nice bacterial genome browser today via “Discovering Biology in a Digital World:” the Genome Projector.Genome Projector The is a map of over 100 bacterial genomes including a circular genome map, a genome map, a pathways map and a “DNAWalk” map. Put in a search term (I put “iron” in here, you know, as in ‘mining for,’ tried gold, but alas.. there is no gold in them thar… anyway…) and the hits show up as numbers in the tabs and pins in the maps. The maps are zoomable (just like GoogleMaps) and the pins are clickable with a popup to links out to databases and more information. It’s not quite as useful or in depth as perhaps IMG as a browser or Reactome or Kegg for pathways, but it’s simple and cool way to browse the genomes for more information and links to databases. Below the fold (continue reading link) are two more screenshots of my search in pathways and zoomed with clicked pin. Continue reading

Finding Flies

I finally got around to reading last month’s Nature paper on the genomic sequence of 12 Drosophila species. In addition to being genomics research (which is my field now :), it is also looking at 12 of the couple dozen species I studied for my Ph.D. (though I was only looking at the evolution of R1 & R2 retroposons in arthropods).Interesting paper, and I might go into it more in depth later (what genomics means and doesn’t mean for evolutionary studies).

But I did get to thinking, where would I go to browse and search the genomic sequence data for these 12 species ( hey, I might want to recreate my work, though the Eickbush lab already has.. and extended). Of course there are the two browsers mentioned in the paper ;-), Flybase and UCSC Genome Browser, though UCSC doesn’t include D. willistoni as I write this. I checked the other two major general genome browsers, as opposed to species or taxa specific: Ensembl and NCBI’s MapViewer. Continue reading