SPELL (Serial Pattern of Expression Levels Locator) is a query-driven search engine for microarray, RNAseq and tiling array data. Given a small set of query genes, SPELL can identify which datasets are most informative for these genes, then within these datasets, additional genes are identified with expression profiles most similar to the query set. SPELL contains more than 5000 experiments from over 300 plus datasets.
You can query certain types of gene data such as expression in tissue and life stage, RNAi phenotypes, allele phenotypes and gene descriptions using the SimpleMine tool. You can paste in a list of gene names of interest or upload a file with gene names.
While the new genome browser (JBrowse) implemented at WormBase has several advantages, like faster browsing and a faceted track selector, it does lack a few features from the venerable GBrowse instance that has been at WormBase for many years. While we and the JBrowse developers are working on addressing those minor shortcomings, this article is about how to circumvent one of those issues now.
JBrowse lacks the ability to make a high resolution image like GBrowse. While taking a screenshot can sometimes result in an acceptable image (for example, Macs with a retina display work pretty well), the result is not always suitable for publication or putting on a poster. The method described here still does not allow for making an SVG image, but it does allow for higher quality PNG images than just taking a screenshot and also allows for the creation of a PDF document with the image in it. Unfortunately, this method requires downloading a tool where we must edit one of the source files and then execute it on the command line. While this is a little bit of a hassle, once it is set up, creating screenshots is quite easy.
We are pleased to introduce a new genome browser that we are currently testing as a replacement for the current, long serving genome browser (GBrowse). The new browser, an implementation of JBrowse from the GMOD project, is currently available at wormbase.org/tools/genome/jbrowse/. The new genome browser has a fast and pliable user interface; becoming oriented to the new browser should be relatively painless as it shares many design features in common with the current browser.
The new genome browser also has new functionality not available in the old one. Key among these are (all of which are available from the genome browser’s file menu):
- Opening many types of data files (GFF, BAM, BigWig/BigBed, VCF), without having to upload them (so it’s *fast*).
- Creating combination tracks, where the contents of any two tracks can be combined using set or arithmetic operations.
- Making a sequence (DNA or amino acid) search track that will highlight when a motif is present (the search string can take the form of regular expressions–please let us know if you’d like help writing a regular expression).
Other useful features include the ability to “pin” a track to the top of the browser so it won’t scroll off the top of the page (simplifying visual comparisons with other open tracks), and a “full page” button that will open a new browser window where the genome browser takes up the full page.
Please try out the new browser and give us any feedback you can think of, either things you’d like to see, things you don’t like, whatever.