Help us by acknowledging WormBase in your publications.

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We would like to enlist your help in ensuring that WormBase continues to exist and is successful. You can do this by explicitly acknowledging WormBase in each of your papers when you have used it in the planning, design, execution, analysis, or reporting of the research described.

This simple task will help us make the case to administrators at NIH and others for the utility of WormBase. You can do this in two ways:

1. Include in your acknowledgments, a statement thanking WormBase, ‘We thank WormBase’. To save characters, it can be included in a list:  ‘We thank XYZ for reagents, ABC for comments and WormBase’. If this is a problem, just mention the particular WormBase release (WSnnn) in the text.  When you use these methods, the acknowledgements of WormBase are amenable to searching and reporting.

2. As a reviewer or editor, you could check that WormBase is acknowledged, if appropriate.

Thanks for your help!

New data: male neural connections in WormBase

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The WS220 release of WormBase contains release 2 of the Male Wiring Project (MWP), at the Albert Einstein College of Medicine. This data consists of neural connections found in the adult male tail. It adds 8,400 pair-wise connections to WormBase , taking the total to 22,500 connections. All neural connection data in WormBase can be accessed using NeuroBrowse, an interactive graphical tool. A link to NeuroBrowse is on the relevant anatomy pages or it can also be directly launched. A brief user guide for NeuroBrowse is on our wiki. We thank MWP for sharing data with WormBase. Please visit the MWP web site for updates and additional information.

Did you know that WormBase provides useful data files for download?

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WormBase maintains a public FTP site where you can find many commonly requested files and datasets, the WormBase software and prepackaged databases. DNA sequence data for the genomes of C. elegans, C. briggsae, C. remanei, etc., are available in FASTA format, as is protein data.  Microarray data like the up-to-date mapping of microarray probes to WormBase genes for Affymetrix, Agilent, Washington University Genome Sequencing Center and Stanford Microarray Database (SMD) chips, is also made available.  For C. elegans, the following files are down-loadable from the FTP site: confirmed_genes — which lists curated C. elegans genes that have been confirmed by transcriptional data; wormpep — FASTA-format files containing predicted and confirmed protein translations, and many other files.

Take a look at our FTP site at ftp://ftp.wormbase.org/pub/wormbase/.  Be sure to look at the README file in each directory for a listing of the contents of that directory.

Genomes in WormBase

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In addition to C. elegans, WormBase provides several resources for viewing and obtaining genome information for different worm species. WormBase classifies genomes in various tiers depending on the amount of curation effort it is able to spend on maintaining them.  For a description of the various genomes either in, or coming to WormBase, their current status and the resources available for each, please visit http://wiki.wormbase.org/index.php/WormBase_Genomes.

WormBase refines method to map RNAi targets to the genome

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During the process of curation of RNA interference (RNAi) data, WormBase routinely maps the targets of any given RNAi experiment to the genome based on information present in the paper that describes the experiment. Recently WormBase has refined this process and addressed inconsistencies in target determination.  Previously, we were not filtering out the highly fragmented hits that occurred. That is, when many very short alignments occurred close together on the genome our mapping script was concatenating these splits, much like it would do when it skips over introns. These hits caused errant primary and secondary targets to be displayed. Most targets for RNAi experiments remain unchanged, but errant hits have been removed from WormBase.
The criteria for primary and secondary target determination (these descriptions are also on the individual RNAi report pages) are as follows:
Primary targets: These are targets that have sequence identity to the RNAi probe of at least 95%, over a stretch of at least 100 nucleotides, identified using a
combination of BLAST and BLAT algorithms.  These are usually the intended target genes of an RNAi experiment.
Secondary targets: These are targets that have between 80 and 94.99% sequence identity over a stretch of at least 200 nucleotides to the RNAi probe. Targets (and overlapping genes) that satisfy these criteria may or may not be susceptible to a RNAi effect with the given probe and represent secondary (unintended) genomic targets of an RNAi experiment.