Three new features added to SimpleMine

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WormBase SimpleMine users can now batch-download chromosome coordinates and transcription factors within 2kb of promoter regions. When searching for interacting genes, there is a new option to exclude high-throughput interaction results.

We have also developed an instance of SimpleMine for the Alliance of Genome Resources for researchers to batch download essential gene information for worm, yeast, fly, Xenopus, zebrafish, mouse, rat, and human. Your feedback on our work is always appreciated! Please email help@wormbase.org.

The clones are back

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Good news for those of you using the C. elegans libraries held at Wellcome Sanger Institute – they have just restarted distribution of the C. elegans clone libraries they hold. The webpage is currently under development, so please email bioresource@sanger.ac.uk directly with your requests.

Please note that some WormBase tools are down

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Please note that because of server upgrades that we are doing the following WormBase tools are not available for use, including the Author First Pass form. We apologize for any inconvenience caused. The following tools are currently out of service:

SimpleMine

Gene Set Enrichment Analysis

Gene Name Sanitizer

Expression Dataset Locator

RNA-Seq FPKM Gene Search

Gene-pair Ontology Graph

Terms Ontology Graph

Wormicloud

SimpleMine Update: Biotype, GO term, RNAi clone and more

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We have added new data fields to SimpleMine, a batch download tool for essential gene information. Users can now access biotype, GO term, and RNAi clones through this simple web interface.

We also added more information to previously existing data fields. All references, including books, reviews, meeting abstracts, and primary research articles, are now listed in the Reference field. For genetic map position, we display error rates of the genetic mapping data. In addition to all “live” gene objects, users can now search for pseudogene or “suppressed” gene objects. 

Changes to the web interface include: improved performance, species-specific or mixed-species searches and a search button for all genes in one species. There are 32 data fields in SimpleMine, organized into five categories so that users can quickly select them. 

Note that WormBase SimpleMine provides essential information for genes in nine nematode species. There is a prototype of the SimpleMine tool for the Alliance of Genome Resources with data related to human, mouse, rat, zebrafish, fly, yeast, and worm (C. elegans only):  https://www.alliancegenome.org/prototypes