Tag Archives: yeast

Tip of the Week: Yeast genome? There is an app for that!

GBrowse navigation basics tutorial from yeastgenome on Vimeo.

The Saccharomyces Genome Database (SGD) has several short video tutorials that introduce basic navigation (shown above), expression data and more.  Each of these tutorials are short, 1-2 minutes, and there are 21 of them (15 on yeastmine alone). If you want to go further in depth, we have a tutorial on the Saccharomyces Genome Database (SGD) (subscription)also that is about an hour long, modular and includes exercises. We have also done tips on Yeastmine and other SGD related tools (open access). You can also find a tutorial at OpenHelix on GBrowse, which is the browser used at SGD. And there is this short 5 minute GBrowse video tutorial.

So, a yeast researcher has no lack for video training on using SGD.

But, today I wanted to introduce you to SGD’s new app for the mobile researcher: YeastGenome App. The app has some pretty decent functionality. As their FAQ enumerates:

yeastgenome-3-newipad

“Saccharomyces Genome Database by gene name or keyword to find fundamental information about your favorite gene. Browse the database by feature type and quickly view fundamental information, sequence information, Gene Ontology, interactions, phenotypes, and references associated with the terms.

Does the app have any other special features?
Yes, you can use the app to save your favorite genes in a convenient list. You can also e-mail yourself or your friends and colleagues any information you find about yeast genes in the Saccharomyces Genome Database.”

I’ve had a go at the app for a bit, and it makes browsing and searching yeast genome data pretty convenient and easy. The app was reported in this year’s Database issue at NAR and it gives a good rundown of the app. Don’t need convincing? Then you can go right to iTunes and get it now.

But this reminds me, I did a feature on mobile apps for genomics research last year that reviewed GeneWall, Wowser and MyGenome and the year before that introduced an app for “moving molecules”. THis new app and several I’ve seen in the interim since those posts suggest that perhaps it’s time to do a new post on mobile apps available for genome research.  Perhaps that will be the next tip of the week from me in a few weeks.

Tip of the Week: cast a SPELL and find your genes!

Today’s tip is on a resource named SPELL, which stands for ‘Serial Pattern of Expression Levels Locator’. You enter a small set of gene names. The SPELL search engine will analyze expression datasets collected from GEO, ArrayExpress, SMD, etc. and tell you which datasets are most informative for your genes. It will also return a list of other genes with similar expression profiles. The spell_logo.jpgresults link to the original publications and to gene summaries at SGD, and provides you with a list of over-represented GO terms. I found SPELL through SGD’s Expression Connection (a wonderful resource in and of itself), and liked what I saw. Plus the name ‘SPELL’ is sort of appropriate for Halloween, which is fast approaching. Read more about the resource here, which is also referenced below.

Reference:
M. A. Hibbs, D. C. Hess, C. L. Myers, C. Huttenhower, K. Li, O. G. Troyanskaya (2007). Exploring the functional landscape of gene expression: directed search of large microarray compendia Bioinformatics, 23 (20), 2692-2699 DOI: 10.1093/bioinformatics/btm403

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.