Team:Queens-Canada/resources

From 2010.igem.org

(Difference between revisions)
Line 9: Line 9:
* [http://worfdb.dfci.harvard.edu/promoteromedb/ Promoterome] contains a comprehensive collection of sequences for promoters that precede known ''C. elegans genes''.  These sequences can be used to design PCR primers to PCR promoters from genomic DNA.
* [http://worfdb.dfci.harvard.edu/promoteromedb/ Promoterome] contains a comprehensive collection of sequences for promoters that precede known ''C. elegans genes''.  These sequences can be used to design PCR primers to PCR promoters from genomic DNA.
* [http://128.122.61.5/cgi-bin/UTRome/utrome.cgi UTRome] and [http://utrdb.ba.itb.cnr.it/ UTRdb] are databases of 3' UTR sequences in ''C. elegans''.  It should be noted that UTRdb includes 3' UTRs for a variety of organisms, and that an advanced search may be necessary to return results specific to ''C. elegans''.
* [http://128.122.61.5/cgi-bin/UTRome/utrome.cgi UTRome] and [http://utrdb.ba.itb.cnr.it/ UTRdb] are databases of 3' UTR sequences in ''C. elegans''.  It should be noted that UTRdb includes 3' UTRs for a variety of organisms, and that an advanced search may be necessary to return results specific to ''C. elegans''.
-
* The [http://www.mirbase.org/cgi-bin/mirna_summary.pl?org=cel MicroRNA Database] contains an extensive record of 175 known ''C. elegans'' MicroRNAs, including sequences, references, and known targets.</div>
+
* The [http://www.mirbase.org/cgi-bin/mirna_summary.pl?org=cel MicroRNA Database] contains an extensive record of 175 known ''C. elegans'' MicroRNAs, including sequences, references, and known targets.<html></div></html>
<html><div class="section"><h2>Protocols and Experimental</h2></html>
<html><div class="section"><h2>Protocols and Experimental</h2></html>
Line 16: Line 16:
* [http://wormbook.org/toc_wormmethods.html WormMethods] is a section of WormBook that contains protocols for working with worms.
* [http://wormbook.org/toc_wormmethods.html WormMethods] is a section of WormBook that contains protocols for working with worms.
* The [http://www.cbs.umn.edu/CGC/strains/ ''Caenorhabditis'' Genetics Center] is a bank of virtually every strain of ''C. elegans'' used in laboratories, including both wild-type strains and behavioral mutants. This site serves as a useful resource, but it should be noted that strains can also be ordered from this site at extremely low cost.
* The [http://www.cbs.umn.edu/CGC/strains/ ''Caenorhabditis'' Genetics Center] is a bank of virtually every strain of ''C. elegans'' used in laboratories, including both wild-type strains and behavioral mutants. This site serves as a useful resource, but it should be noted that strains can also be ordered from this site at extremely low cost.
-
* The Chin-Sang Lab (in which we conducted most of our lab work) has [http://130.15.90.245/lab_protocols.htm a wealth of worm-relevant protocols], and links to other protocol resources (such as [http://www.protocol-online.org/prot/Model_Organisms/C__Elegans/index.html Protocols Online] and [http://cshprotocols.cshlp.org/ Cold Spring Harbor Protocols]) that have been honed and tested to perfection. We consider them particularly indispensable, as well as easy to follow.</div>
+
* The Chin-Sang Lab (in which we conducted most of our lab work) has [http://130.15.90.245/lab_protocols.htm a wealth of worm-relevant protocols], and links to other protocol resources (such as [http://www.protocol-online.org/prot/Model_Organisms/C__Elegans/index.html Protocols Online] and [http://cshprotocols.cshlp.org/ Cold Spring Harbor Protocols]) that have been honed and tested to perfection. We consider them particularly indispensable, as well as easy to follow.<html></div></html>
<html><div class="section"><h2>Summaries and Functional Descriptions</h2></html>
<html><div class="section"><h2>Summaries and Functional Descriptions</h2></html>
Line 22: Line 22:
* [http://wormbook.org/ WormBook] is a functional overview of worm physiology and genetics, with an emphasis on development.  It began as an online version of [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=ce2 ''C. Elegans'' II], the standard textbook for worm research, and has been frequently updated since.
* [http://wormbook.org/ WormBook] is a functional overview of worm physiology and genetics, with an emphasis on development.  It began as an online version of [http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=ce2 ''C. Elegans'' II], the standard textbook for worm research, and has been frequently updated since.
* [http://wormweb.org/neuralnet#c=BAG&m=1 NeuralNet] contains visual representations of C. elegans' neural network.  It is useful for determining an appropriate neuron to modify in order to illicit a desired behavioral response.
* [http://wormweb.org/neuralnet#c=BAG&m=1 NeuralNet] contains visual representations of C. elegans' neural network.  It is useful for determining an appropriate neuron to modify in order to illicit a desired behavioral response.
-
* [http://wormatlas.org/ WormAtlas] focuses on an anatomical overview of both hermaphroditic and male worms. WormBook occasionally makes assumptions about the reader’s knowledge that can be remedied with a quick visit to WormAtlas.</div>
+
* [http://wormatlas.org/ WormAtlas] focuses on an anatomical overview of both hermaphroditic and male worms. WormBook occasionally makes assumptions about the reader’s knowledge that can be remedied with a quick visit to WormAtlas.<html></div></html>
{{:Team:Queens-Canada/foot}}
{{:Team:Queens-Canada/foot}}

Revision as of 17:49, 24 October 2010

Review of Online Resources

Sequences and Gene Information

  • WormBase is the primary resource for the genome of C. elegans and other related nematodes. It contains sequences for coding regions, expression information, descriptions of genes, and ready access to many other analyses and tools hosted by NCBI. WormBase is not efficient for navigating the whole genome sequence of C. elegans, however; for raw sequences, we prefer NCBI’s copy of the chromosomes, especially since it frequently links back to WormBase. WormBase also does not contain expression strength information for constitutive promoters. This can be obtained from AceView at NCBI.
  • GFPWorm has visual information on C. elegans expression patterns. This is indispensible when looking for tissue- or stage- specific promoters and UTRs, and cross-references WormBase at every opportunity.
  • Promoterome contains a comprehensive collection of sequences for promoters that precede known C. elegans genes. These sequences can be used to design PCR primers to PCR promoters from genomic DNA.
  • UTRome and UTRdb are databases of 3' UTR sequences in C. elegans. It should be noted that UTRdb includes 3' UTRs for a variety of organisms, and that an advanced search may be necessary to return results specific to C. elegans.
  • The MicroRNA Database contains an extensive record of 175 known C. elegans MicroRNAs, including sequences, references, and known targets.

Protocols and Experimental

  • The Worm Breeder's Gazette is a non-refereed, biannual publication dedicated to C. elegans and other nematodes. It is hosted at WormBook and serves as a community journal. Articles frequently focus on new and useful techniques, which might get lost if they were presented in more general journals, but may prove to be of great utility in synthetic worm biology.
  • WormMethods is a section of WormBook that contains protocols for working with worms.
  • The Caenorhabditis Genetics Center is a bank of virtually every strain of C. elegans used in laboratories, including both wild-type strains and behavioral mutants. This site serves as a useful resource, but it should be noted that strains can also be ordered from this site at extremely low cost.
  • The Chin-Sang Lab (in which we conducted most of our lab work) has a wealth of worm-relevant protocols, and links to other protocol resources (such as Protocols Online and Cold Spring Harbor Protocols) that have been honed and tested to perfection. We consider them particularly indispensable, as well as easy to follow.

Summaries and Functional Descriptions

  • WormBook is a functional overview of worm physiology and genetics, with an emphasis on development. It began as an online version of C. Elegans II, the standard textbook for worm research, and has been frequently updated since.
  • NeuralNet contains visual representations of C. elegans' neural network. It is useful for determining an appropriate neuron to modify in order to illicit a desired behavioral response.
  • WormAtlas focuses on an anatomical overview of both hermaphroditic and male worms. WormBook occasionally makes assumptions about the reader’s knowledge that can be remedied with a quick visit to WormAtlas.