Searching WormBase for Information about Caenorhabditis elegans

Erich M. Schwarz1, Paul W. Sternberg2

1 California Institute of Technology, Pasadena, California, 2 Howard Hughes Medical Institute, California Institute of Technology, Pasadena, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 1.8
DOI:  10.1002/0471250953.bi0108s14
Online Posting Date:  July, 2006
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Abstract

WormBase is the major public biological database for the nematode Caenorhabditis elegans. It is meant to be useful to any biologist who wants to use C. elegans, whatever his or her specialty. WormBase contains information about the genomic sequence of C. elegans, its genes and their products, and its higher‐level traits such as gene expression patterns and neuronal connectivity. WormBase also contains genomic sequences and gene structures of C. briggsae and C. remanei, two closely related worms. These data are interconnected, so that a search beginning with one object (such as a gene) can be directed to related objects of a different type (e.g., the DNA sequence of the gene or the cells in which the gene is active). One can also perform searches for complex data sets. The WormBase developers group actively invites suggestions for improvements from the database users. WormBase's source code and underlying database are freely available for local installation and modification.

Keywords: Caenorhabditis elegans; WormBase; nematode; genomic annotation; gene expression pattern; RNAi; neuronal connectivity

     
 
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Table of Contents

  • Basic Protocol 1: Navigating the WormBase Home Page
  • Basic Protocol 2: Performing a Database Search
  • Basic Protocol 3: Examining a Gene in C. elegans
  • Basic Protocol 4: Examining a Molecular Sequence in C. elegans
  • Basic Protocol 5: Finding Protein Features
  • Basic Protocol 6: Searching for Gene Products with Particular Sequence Motifs
  • Basic Protocol 7: Using the Genome Browser
  • Basic Protocol 8: Viewing the C. briggsae Genome and its Synteny with C. elegans
  • Basic Protocol 9: Finding Sequence Similarities with Blast
  • Basic Protocol 10: Mining Gene Data with WormMart
  • Basic Protocol 11: Downloading a Batch of Sequences
  • Basic Protocol 12: Examining the Genomic Content of a Classical Genetic Interval
  • Basic Protocol 13: Using Other WormBase Searches
  • Alternate Protocol 1: Installing and Running WormBase Locally
  • Guidelines for Understanding Results
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

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Figures

Videos

Literature Cited

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Key References
   Brenner, 1974. See above.
  The beginning of modern C. elegans research, this article remains vividly readable and gives a clear introduction to the goals and tactics of worm genetics.
   C. elegans Sequencing Consortium, 1998. See above.
  This summarizes the first findings from the near‐completion (∼98%) of the C. elegans genome, and gives useful background information about how the genomic sequence was acquired and organized. (Final closure of the last 2% of gaps in the genome sequence was achieved in November 2002, four years later.)
   Harris et al., 2004. See above.
  Gene Ontology has become a recognized common vocabulary for functionally annotating gene products in both WormBase and many other genomic databases.
   Mulder et al., 2005. See above.
  Like Gene Ontology terms, InterPro motifs have become a common vocabulary for genome annotation in WormBase and elsewhere.
   Stein et al., 2002. See above.
  The genome browser described here is extensively used in WormBase.
   Sulston et al., 1983. See above.
  The lineage browser in WormBase is an attempt to provide a Web interface for small slices of the entire set of findings given here.
   White et al., 1986. See above.
  The neuronal connections and anatomy stored in WormBase are largely derived from this work.
Internet Resources
  http://wormbase.org
  The main Web site for WormBase. It is meant to be slightly less bleeding‐edge than the development site, but to be maximally stable.
  http://dev.wormbase.org
  The development Web site for WormBase. This site runs the latest release of the WormBase data, allowing any bugs in the data or their presentation to be caught before being put on the main site. If one wants the absolutely latest information on C. elegans, this is therefore the site to use (the main site lags by two weeks, the interval between successive data releases). New additions to the site software are tested here first as well.
  http://www.wormbook.org
  WormBook is an online anthology of over 70 articles reviewing a great deal of current knowledge about C. elegans biology in 2005. All articles are provided in both HTML and PDF format, and are freely downloadable. Along with its two predecessors (Wood, ; Riddle et al., ), WormBook is strongly recommended for anybody starting work on this organism or studying it.
  http://ws150.wormbase.org
  The Web site for the archival WS150 release of WormBase's data. The advantage of this site is that the data do not change, and thus can be used for reliable cross‐comparison of bioinformatical analyses by different research groups at different times. Similar sites exist for several previous tenth releases (e.g., WS140: http://ws140.wormbase.org) and future archival sites are planned for roughly once every 7 months.
  http://www.its.caltech.edu/∼wormbase/userguide
  The User's Guide for WormBase.
   ftp://ftp.wormbase.org/pub/wormbase
  This FTP site contains archives of the wormpep and wormrna files, and the core software for running WormBase as a local installation.
  http://caltech.wormbase.org
  The California Institute of Technology mirror site for WormBase maintained by Erich Schwarz (emsch@its.caltech.edu).
  http://imbb.wormbase.org
  The Greek mirror site for WormBase, maintained by Nektarios Tavernarakis (tavernarakis@imbb.forth.gr).
  ftp://ftp.sanger.ac.uk/pub2/wormbase
  This FTP site contains the complete releases of WormBase's data (typically the most recent two, along with permanently archived releases such as WS100 through WS150).
  http://www.wormatlas.org
  The public atlas of C. elegans anatomy, with several key references for worm anatomy on line, including White et al. ().
  http://elegans.swmed.edu
  A useful site with links to worm literature and genetic strain information, maintained by Leon Avery (leon@eatworms.swmed.edu).
  http://wormbase.org/about/about_Celegans.html
  Links to several other C. elegans databases are collected here.
  http://www.geneontology.org
  This site gives extensive documentation for the Gene Ontology system, increasingly used for functional annotation in WormBase.
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