WS267 release of WormBase
Please note that the WS267 release of WormBase is now live.
Trichuris muris update
Trinity assembled RNASeq reads from publicly available short read data at SRA have been added to Trichuris muris as additional track and alignments. In addition IsoSeq data from long-range PacBio data (provided by the Berriman lab), corrected by genome alignment has been used as additional source to build transcript models.
In addition the Trichuris muris ncRNA gene set has increased from 26 to 759 following the integration of data produced by the WormBase Parasite ncRNA prediction pipeline. These transcripts have been fully integrated with ...
Source: WormBase - November 12, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news release notes WS267 Source Type: news
WormBook in GENETICS
From Iva Greenwald:
Three years ago, I announced in this column the creation of WormBook in GENETICS, thanks to a generous funding commitment to our community by the Genetics Society of America.
Please look at what we’ve done so far and you’ll see what a great resource it is: http://www.genetics.org/content/wormbook
We are really hitting our stride now, and you will see WormBase announcements of new chapters increasing apace. The more you demonstrate the value of WormBook through viewing, downloading, and especially, citing the articles, the more the GSA will understand the value of their sponsorship and be incline...
Source: WormBase - October 17, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news
New chapter of WormBook in GENETICS
Check out the new chapter of WormBook in GENETICS: From “the Worm” to “the Worms” and Back Again: The Evolutionary Developmental Biology of Nematodes by Eric Haag, David Fitch and Marie Delattre. (Source: WormBase)
Source: WormBase - October 5, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news wormbook Source Type: news
WS266 release
Please note that the WS266 version of WormBase has been released. Go to the release notes for this release to view a list of data types and their numbers. A list of all files available on our FTP site can also be viewed. Changes in this release include the following:
Physical Interaction data curation
We have added over 5000 manually curated physical interactions which include binary protein-protein interactions as well as protein interactions that occur in a protein complex. Protein-protein interaction data can be found as a part of physical interaction data in the Interactions widget on the gene page. The Interactions ...
Source: WormBase - September 18, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news release notes WS266 Source Type: news
Paper of Interest: OrthoList 2
The new comparative genomic analysis between C. elegans and humans, OrthoList 2 (OL2), was just published early online in GENETICS. OL2 comes with a new web-based tool that allows for rapid searches of OL2 by worm or human gene identifiers, protein domains (InterPro and SMART), or human-disease associations (OMIM), and also includes updated RNAi resources. The paper describes OL2 and various findings, including how the content of OL2 compares with the original OrthoList tool. The web-based tool for accessing OL2 is here. (Source: WormBase)
Source: WormBase - August 22, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: news paper of interest orthologs Source Type: news
WS265 release
loci with two different protein products
There are a small number of loci which code for two very different protein products. These include dicistronic mRNA operons and loci which have a few small exons in common then have alternate splicing leading to many different exons being used.
The details of some of these can be found in the WormBook chapter “Operon and non-operon gene clusters in the C. elegans genome”.
Previously, these have been curated as isoforms of a single gene. This was causing problems because the description of gene
function would be based on one isoform, leaving the other isoform undescribed...
Source: WormBase - July 20, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news release notes WS265 Source Type: news
Check out the latest chapter on microRNAs in WormBook
Check out the latest chapter in WormBook, GENETICS: Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs by Victor Ambros and Gary Ruvkun. (Source: WormBase)
Source: WormBase - July 5, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news paper of interest wormbook Source Type: news
High throughput datasets in SPELL now searchable based on topic
Data sets coming from high throughput experiments which reside in SPELL have now been updated with topics so that you can actually search by your favorite topic. You can see the topic search options by clicking the button ‘Options for Filtering Results by Dataset Tags‘ on the SPELL home page under the search box for Gene Name(s). (Source: WormBase)
Source: WormBase - May 22, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication new features news tutorials high throughput dt SPELL Source Type: news
Which WB tool to use -check out our updated list and links
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. (Source: WormBase)
Source: WormBase - May 18, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news tutorials tools Source Type: news
Guest Blog: New Nematodes in WormBase
This WS264 release of WormBase includes two new genome assemblies from both a free-living Caenorhabditis species (C. nigoni) and a whipworm parasite of mice (Trichuris muris).
The C. nigoni genome was assembled from both long-read (Pacific Biosciences) and short-read (Illumina) data, and then further scaffolded by genome-wide alignment with its very close relative, C. briggsae.
Despite the fact that C. nigoni and C. briggsae are closely enough related to produce partially fertile offspring, their lifestyles and genomes are quite different. C. briggsae, like C. elegans, is primarily a self-fertilizing hermaphrodite...
Source: WormBase - May 16, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: news guest WS264 Source Type: news
Check out the Eukaryotic Genomic Databases book!
The Eukaryotic Genomic Databases book has just been released by Springer (Editors: Kollmar, Martin) and contains detailed chapters related to the eukaryotic databases such as WormBase, FlyBase, the yeast databases, SGD and PomBase, etc. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research. (Source: WormBase)
Source: WormBase - May 15, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication external website news paper of interest tutorials book genomes Source Type: news
WS264 release
C. elegans sORFs
sORFs.org is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq).
It contains predicted sORF regions for several species, including C. elegans.
We have annotated 118 predicted sORF regions as coding (CDS) isoforms of the existing genes. It is likely that in the next release, where these isoforms do not overlap with existing isoforms, these sORF regions will be changed to be individual genes and not isoforms.
52 of these annotated sORF regions do not start with the canonical Methionine AUG initiation codon. It is possible that they use a non-canonical initiat...
Source: WormBase - May 14, 2018 Category: Genetics & Stem Cells Authors: Michael Paulini Tags: new datasets news release notes new release WS264 Source Type: news
Include strain names in publications!
We urge you to explicitly state strains used in your experiments to foster reproducibility and to help WormBase biocurators get your results into WormBase.
Historically, C. elegans researchers just stated the alleles used, based on the reasonable idea that all strains were close to Brenner’s N2. As the years and hundreds of worm generations passed, strains diverged. We usually don’t know the full genotype of our strains (and really won’t even with whole genome sequencing since copy number variation is often hard to detect). Including strain names will greatly help sort out any background effects that are realiz...
Source: WormBase - April 26, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication community news data request strain Source Type: news
Wondering how to cite WormBase?
If you are looking to cite WormBase please take a look at: https://wormbase.org/about/citing_wormbase#012–10. This can also be accessed from the Menu at the bottom of the WormBase home page on the extreme left, under WormBase–>How to cite. Please do explicitly acknowledge WormBase in your published work when you have used it in the planning, design, execution, analysis, or reporting of the research described. We can then search for these acknowledgements and use these numbers in various reports, eg. for funding agencies, etc. (Source: WormBase)
Source: WormBase - April 25, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news Source Type: news
Please specify allele and strain names in publications
WormBase curates data from published papers and attaches different types of data such as phenotype, overview, expression, human disease model, etc., to genetic entities such as genes, alleles, strains or transgenes. These are also bonafide ‘objects’ in our database which allow us to attach data to them. If we cannot find these named genetic entities in your paper it becomes extremely difficult for us to curate the paper. It is not enough to just specify the amino acid or nucleic acid change of a mutation, we need either the strain or allele name to curate the paper. (Source: WormBase)
Source: WormBase - April 10, 2018 Category: Genetics & Stem Cells Authors: Ranjana Kishore Tags: brief communication news data request paper Source Type: news
