Check out our new tissue enrichment analysis tool!

We are pleased to announce our new web-based tool ‘TEA‘, this tool has been developed for identifying enrichment of C. elegans tissues among gene sets.  The software is also available for download.  Description of the tool is published here.

Introducing a new genome browser for WormBase

JBrowse

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):

  1. Opening many types of data files (GFF, BAM, BigWig/BigBed, VCF), without having to upload them (so it’s *fast*).
  2. Creating combination tracks, where the contents of any two tracks can be combined using set or arithmetic operations.
  3. 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.

WormBase release WS248

The newly released WS248 version of WormBase includes several updates based on curation topics as well as synchronisation with other databases.
In addition the use of Gene Ontology has been extended.

microRNA update for Brugia malayi

The newest data on Brugia malayi microRNAs from miRBase Release 21 has been integrated,
which includes pre-miRNA and mature transcripts as well as the consolidation of
nomenclature used by WormBase and miRBase.

Heavy Metal Topic curation

This release focuses on the curation of data related to Heavy Metal response in nematodes.
Supporting data and publications have been added to WormBase, in addition to review of
gene models for genes involved in this pathway.

New automated descriptions

Gene descriptions generated automatically using a new in-house pipeline were rolled out
for C. elegans in the WS247 release. This release extends that to all other core
species (B. malayi, O. volvulus, C. briggsae, C. brenneri, C. remanei, C. japonica)

New Gene Ontology Annotation Class

Starting with the WS248 release, Gene Ontology annotations will be represented in a new class,
GO_annotation. The GO_annotation class modelsGO annotations as distinct objects in the
database and allows for richer representation of GO data. For example, the GO_annotation
class contains information on interacting genes for annotations that use the IGI (Inferred
from Genetic Interaction) and IPI (Inferred from Physical Interaction) evidence codes, and
also contains annotation extensions that provide additional context for GO terms, such as
substrates for enzymatic activities. The GO_annotation class also includes annotations from
external groups such as UniProt and the Gene Ontology Consortium’s phylogenetic annotation
efforts using PAINT.

WormBase release WS247

Orthology update

* Data from Inparanoid was updated to version 8
* Orthology data for all core nemtatodes and model organisms was imported from WormBase Parasite release 1
* OMA and TreeFam data was removed in preparation for an update (TreeFam accessions will remain as database crossreferences)

Expression and Picture update

* A large set of expression graphs for other nematodes produced by Yanai’s has been added

RNASeq data

The RNASeq data will become richer in WS247.

There will also be “control” mean and median FPKM values derived from the data which does not have a specific experimental condition applied.

New/updated reference genomes

This release we see a rebuild of C. elegans, B. malayi and O. volvulus. Various data classes and curational activites have been undertaken on these species since the release of WS246