Tag Archives: genome

Tip of the Week: Model Organism Database tutorials

gbrowseFor the tip of the week today, we’d like to point out a number of new (free to you) tutorials on model organism database resources. These seven tutorials (include flash movie tutorial, slides for downloading, exercises and handouts) were partly funded by a NHGRI grant. We just put out a press release on this, but I thought the Tip of the Week would be a great place to introduce you to these tutorials. We have seven tutorials that are (or will soon be) publicly available (this link takes you to a list and links to all these tutorials). The first four available are on GBrowse, WormBase, RGD (Rat Genome Database) and MGI (Mouse Genome Informatics. GBrowse (the tutorial linked to here), was developed by the Generic Model Organism Database (GMOD) project and is a great tool to develop genome browsers for model and research organisms. Many model organism databases use GMOD resources in full or part, including many of the ones we have tutorials on here. Three more will be coming very soon on ZFIN (Zebrafish), FlyBase (Drosophila) and SGD (yeast). Check them out :).

Tip of the Week: RGD's GViewer

This week has been quite busy here at OpenHelix and the U.S. For the tip of this week, as we do occasionally, I’m going to highlight a short tutorial tip done by someone else. This week’s is one done by the developers of RGD and showing the uses of the GViewer. This tutorial is at SciVee, as the description states:

The rat genome comes to life through the use of the Gviewer tool. This video will show you how to use this helpful tool within the RGD website at http://rgd.mcw.edu/. Genes, QTLs, and species syntenies of interest can all be visualized with ease as the Gviewer zooms in and navigates through the rat genome with a few clicks.

Friday Fun: Quilting the Genome

genome quiltSo, in the spirit of friday fun where we’ve done  puzzles, genome music and other fun stuff (so, ok, not always on Friday), I thought I’d show you an interesting site: Genome Quilts. The creator of these quilts created a one genome quilt legendsquare pattern for each nucleotide and then quilts these squares in order of a particular gene (the one to the left is this one I believe). So, as an example she posts what I’ve included on the right. Some beautiful quilts. Genomics can be beautiful. So, now I’m thinking, I like to knit… I wonder what patterns I could do for nucleotides or amino acids… hmm, could be a mess, or beautiful. I’ll have to think about that one.

New Online Tutorials on ZFIN, SGD, PlantGDB and GBrowse Resources

Comprehensive tutorials on the model organism databases ZFIN, SGD and PlantGDB and GBrowse, a model organism genome browser, enable researchers to quickly and effectively use these invaluable resources.

Seattle, WA September 15, 2008 — OpenHelix today announced the availability of new tutorial suites on several model organism resources including Zebrafish Information Network (ZFIN), Saccharomyces Genome Database (SGD) and the Plant Genome Database (PlantGDB) and also a tutorial using genome browsers with GBrowse. These four tutorials expand OpenHelix’s model organism database training which now also includes tutorials on MGI (mouse), FlyBase (drosophila), Gramene (grasses), RGD (rat), WormBase and more to come soon. Model organisms are integral to our understanding of basic biology and modern biomedical research. ZFIN is a collection of data, tools, and resources on the zebrafish (Danio rerio), a popular model organism for developmental biology and genetics research and SGD is a collection of data, tools and analyses centered around Saccharomyces cerevisiae, commonly known as bakers’ or budding yeast. PlantGDB is the primary resource for plant comparative genomics.

Additionally, OpenHelix has added a tutorial on GBrowse, a web application that allows you to explore genomic sequences together with annotated data. GBrowse is rapidly becoming the genomic browser of choice amongst model organism databases, because the browser is both universal and yet customizable.

The tutorial suites, available for single purchase or through a low-priced yearly subscription to all OpenHelix tutorials, contain a narrated, self-run, online tutorial, slides, handouts and exercises. With the tutorials, researchers can quickly learn to effectively and efficiently use these resources. These tutorials will teach users:

ZFIN

  • to perform effective searches and understand the displays
  • to access advanced searches enabling multifaceted queries
  • to use the various databases of genes and markers, expression data, mutant genotype/phenotype details, ontologies, and more
  • to investigate many related resources associated with ZFIN

SGD

  • to navigate the SGD site, locate Basic and Advanced Search options, and use the site map to access additional search tools
  • perform the two Basic SGD Quick and Text Search types and understand the displays
  • to navigate the SGD Locus Page and access data from a variety of tools, tabs, and links
  • to investigate many related resources associated with SGD

PlantGDB

  • to perform quick searches and navigate sequence pages
  • to conduct BLAST searches across several plant species of your choice
  • to create exon/intron gene predictions and sequence alignments
  • to construct tables displaying highly varied information from many datasets
  • GBrowse

  • the basic layout and search methods at GBrowse
  • how to access detailed annotation data tied to genomic sequences
  • how to select and customize annotations using Tracks
  • how to upload and incorporate your own data or other external data sources
  • take a tour of different GBrowse installations at model organism databases

To find out more about these and other tutorial suites visit the OpenHelix Tutorial Catalog and OpenHelix or visit the OpenHelix Blog for up-to-date information on genomics.

Tip of the Week: GVS

gvs intro tip This is another tutorial at SciVee (click on image to go to SciVee and watch movie), but this time it’s one of mine I did earlier. I’m on vacation (in Germany, were we used to live in Heidelberg while I worked at EMBL) so I’m pointing you to this short intro I did earlier so I can get back to my weiss wurst). Of course, I’ve also done a tip on one specific aspect of GVS before that you might want to check out. This is a general introduction to the Genome Variation Server at the University of Washington. Additionally, you can get more freely available training materials on GVS including a longer introductory tutorial (40 minutes), slides, handouts and exercises at OpenHelix GVS Tutorial or visit the resource at GVS.

Laying Eggs

platypusThat is what Platypus do, even as mammals :). Two days ago the Platypus genome was published in Nature. So if you haven’t already read it, might be worth a skim at least. So, they aren’t model organisms and not a medically or agriculturally important animals (unless someone starts figuring out how to cook platypus omelets), but platypus (platypi?) do hold a fascinating place in evolutionary history having mammalian (milk, fur) and reptilian (eggs, venom) characteristics. Their genome obviously holds clues to some of this unique history.

For example, the eggs and fertilization genes can tell us a bit of how that evolved…

Continue reading

Wikification of Genbank

Speaking of Genbank’s 25th, a few weeks ago Science had a news piece “Proposal to ‘Wikify’ Genbank Meets Stiff Resistance.” Apparently, those in the Mycology research community have found many inaccuracies in the Genbank records and wish to see a change that would allow annotations to be made by the community:

a scheme like those used in herbaria and museums, where specimens often have multiple annotations: listing original and new entries side by side. It would be a community operation, like Wikipedia, in which the users themselves update and add information, but not anonymously.

But the idea is meeting resistance from Genbank’s Managers:

Continue reading

Miscanthus genome will "fuel" advances

miscanthusI am still digesting (so to speak) the conference I went to the last couple days at JGI. The thrust of the conference was the sequencing and study of genomes (both biomass fuelstock and bacteria/fungus digesters :)) to help create a liquid fuel source for our energy needs. I found it to be a fascinating conference and will definitely write more about it early next week.

For now, I’d like to point you to the work being done on the Miscanthus genome. This is a fascinating plant and possibility for a fuel source. It’s more productive than Switchgrass (and corn and sugar), it has no known diseases or pests (though that will change when/if it becomes a major crop), it is perennial needing much less fertilizer/pesticide input, it grows by rhizomes and sequesters carbon in the ground, it would take much less land to supply liquid fuel needs, it is drought resistant and it can cure cancer. Ok, so the last is not true. Yet, it is a very promising plant. The genome is being sequenced to help scientists and growers determine ways to domesticate it better and to solve the “big” problem… the expense of converting the cellulose to fuel (which is also the topic of metagenomic and genomic research on bacteria at JGI).

Dividends from the chicken genome

Gallus gallusJust saw on the GenomeWeb Daily News that: 

 “Researchers at Michigan State University, the University of Delaware, and Texas A&M worked with funding from the USDA’s Cooperative State Research, Education, and Extension Service to identify individual genes that are linked to MDV, or Marek’s disease, a highly contagious viral disease that costs the worldwide poultry industry $1 billion per year.”

 It makes me very happy to see articles like this, for multiple reasons. First off, it is evidence that our expenditures for “a genome a day” actually do result in public benefit. I really hope the news media picks up this success story – we could use more public support for funding research. 

Second… Continue reading

A genome a day

I want to say ‘keeps the ? away” but can’t think of anything. This is just a quick post. Mary’s first line on the corn genome post, “sometimes it feels like ‘another day, another genome‘ round here got me to thinking”, it isn’t so far off the mark. According to GOLD there are 905 ongoing eukaryotic genomes (according to Entrez Genome Project,  it’s 225, but those are only ones reported to NCBI). The cost of sequencing and completing a genome has drastically decreased. For example, Illumnia recently reported sequencing a human genome in 1 month for $100,000.

Continue reading