If you’re wondering which WormBase tool to use for your data needs, check out this updated list of tools with short descriptions for what to use them for. Click on the tool names to be taken directly to the tool.
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.