The OpenHelix Blog

Welcome to our Friday feature link dump: 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…

• ROFL: Marriage vs PhD illustrated comparison. Hat Tip James. [Mary]
• DGV: Database of Genomic Variants newsletter arrives for March.  Nearly 30k CNVs at this time. They are now releasing annotations to the new human assembly (hg19 or GRCh37).  You can see the newsletter here (warning, PDF). [Mary]
  
• Want to catalog leaves from plants around the world? There’s an app for that: Leafview (hattip: ABW) [Trey]
• The beginning of a long battle: Federal Judge Rules Against Patents On Human Genes . [Trey]
• Ever wonder why the Department of Energy has a Joint Genome Institute? Here’s why. [Trey]
• Sean Eddy on HMMR help, reading documentation, and more in his blog post at Cryptogenomicon. [Jennifer]
• ‘nother day, ‘nother genome: Zebra Finch. While you are looking into genomes, Nature has an interesting 10 year retrospective of the completion of the Human genome. [Trey]

Today’s tip of the week introduces a new (to us) tool for genomic comparisons. We came across this tool reading a blog post at James and the Giant Corn (great blog) about a figure from his research proposal. See, there are reasons to read blogs . The tool he uses to create this figure and analysis is GeVo at CoGe which has several useful tools in addition to GeVo. In today’s tip of the week, we’ll take a quick look at James’ figure at GeVo and introduce CoGe. Check them out, they look like quite useful tools. (and while you’re at it, check out  James’ blog. Tidbits like this and interesting discussions make it well worth it.)

I had a Basset Hound growing up. His name was Useless, Useless S. Grunt. Well, actually it was formally Ulysses S. Grant because the US Kennel Club wouldn’t accept Useless S. Grunt as a name as they felt it was too demeaning. Not sure if they felt it was demeaning to the dog or to the president, but that’s neither here nor there is it?

So,you ask, what made me think of that long-passed sweet dog that tripped over it’s too-long ears with it’s too-short legs? It turns out that they found out what genetic cause there was for those short legs in Basset Hounds (and Dachshunds and other breeds).

As NHGRI’s press release states:

In a study published in the advance online edition of the journal Science, the researchers led by NHGRI’s Elaine Ostrander, Ph.D., examined DNA samples from 835 dogs, including 95 with short legs. Their survey of more than 40,000 markers of DNA variation uncovered a genetic signature exclusive to short-legged breeds. Through follow-up DNA sequencing and computational analyses, the researchers determined the dogs’ disproportionately short limbs can be traced to one mutational event in the canine genome – a DNA insertion – that occurred early in the evolution of domestic dogs.

The insertion turns out to be a retrogene, which of course I also find interesting in that I studied retrotransposable elements. Reverse transcriptase has this habit of reverse transcribing RNA into DNA which can get reinserted back into the genome (hence processed pseudogenes of course).

The study is interesting for two reasons (other than because I had a Basset Hound and studied the evolution of retroelements , it gives us a further clue into evolutionary events that lead to large changes in morphology and the role of retrotranscription and it gives us a clue into possible human conditions.

For more about dog genome, you can read our several posts about the dog genome, go to NCBI’s dog genome home site (or UCSC or Ensembl and other browsers) and read the paper (needs a subscription of course, it’s in Science). It’s an interesting read so far (I want to find some time to read it more fully, perhaps Useless doesn’t live up to his name.. he didn’t really even then ).

Recently, we are learning a lot about the cold virus. The genomes of many have now been sequenced (that is a subscription-required Science report, you can read more about the report here).

You can find more genomic information at the picornaviridae.com at the NCBI’s Entrez Genomes and some structural information at MMDB. (just a side note, rhinovirus is now classified as enterovirus).

For 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 .

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.

So, 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 square 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.

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.

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.

That 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…