Useful Links

Everything you need to know about worms

• WormBook- a comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans (C. elegans) and other nematodes. www.wormbook.org/ 

• WormClassroom- An education portal to the model research organism Caenorhabditis elegans. www.wormclassroom.org

• WormBase- the biology and genome of C. elegans. Includes links to worm community forums and wormbase wiki.www.wormbase.org

• AceView WormGenes- AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences. www.ncbi.nlm.nih.gov/IEB/Research/Acembly/index.html?worm

• C. elegans II- Cold Spring Harbor Laboratory Press. Editors: Donald L. Riddle, University of Missouri, Columbia,Thomas Blumenthal,Indiana University, Barbara J. Meyer, University of California, Berkeley, James R. Priess, Howard Hughes Medical Institute Fred Hutchinson Cancer Research Center, Seattle. www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=ce2 

• Parasitic Nematode Sequencing Project- genome sequencing center. www.nematode.net/index.php

• C. elegans WWW server- provides links to literature, labs and other C. elegans related material. elegans.swmed.edu

Databases and Libraries

• The Worm Image Database- view and download thousands of unpublished electron micrographs and associated data.www.wormimage.org 

• WormAtlas- a database of behavioral and structural anatomy. www.wormatlas.org 
  

• RNAi Database- provides access to results from RNAi interference studies in C. elegans , including images, movies, phenotypes, and graphical maps. rnai.org

• PhenoBank Database- search for genes and phenotypes. www.worm.mpi-cbg.de/phenobank2/cgi-bin/MenuPage.py

• Interactome Database- vidal.dfci.harvard.edu/interactomedb/i-View/interactomeCurrent.pl

• n-Browse- an interactive graphical browser for molecular interaction networks. nematoda.bio.nyu.edu:8080/NBrowse/N-Browse.jsp?last=false

• IntAct- provides a freely available, open source database system and analysis tools for protein interaction data.www.ebi.ac.uk/intact/main.xhtml

• BioGrid- general repository for interaction datasets. www.thebiogrid.org

• EDGE Database- C. elegans differential gene expression database. edgedb.umassmed.edu

• C. elegans SAGE libraries- tock.bcgsc.bc.ca/cgi-bin/sage170

• NEXT Database- the Nematode expression pattern database. nematode.lab.nig.ac.jp/index.html

• Stanford Microarray Database- smd.stanford.edu/index.shtml

• RCSB Protein Data Bank- contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies. www.pdb.org

• NCBI Gene Expression Omnibus- a public functional genomics data repository supporting MIAME-compliant data submissions. www.ncbi.nlm.nih.gov/projects/geo

• EBI ArrayExpress- uses curated, re-annotated subset of data from the Archive to provide information about gene expressionunder various biological conditions. www.ebi.ac.uk/arrayexpress

• Pristionchus pacificus- www.pristionchus.org

• Entrez Gene- a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene 

• UCSC Genome Browser- genome.ucsc.edu/cgi-bin/hgGateway?hgsid=85966288&clade=worm&org=0&db=0

• UniProt- provides the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. www.pir.uniprot.org

• InParanoid- Eukaryotic ortholog groups. inparanoid.sbc.su.se

• OrthoMCL- Ortholog grouping for protein sequences from multiple genomes- orthomcl.cbil.upenn.edu

• TreeFam- a database of phylogenetic trees of animal genes. www.treefam.org

• Reactome- a curated knowledgebase of biological pathways. www.reactome.org/cgi-bin/frontpage?DB=gk_current&FOCUS_SPECIES=Caenorhabditis+elegans&.cgifields=MULTISPECIES

• MetaCyc- a database of nonredundant, experimentally elucidated metabolic pathways. metacyc.org

• KEGG- Wiring diagrams of molecular interactions, reactions, and relations. www.genome.jp/kegg/pathway.html

• Gene Ontology- provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data.www.geneontology.org/index.shtml

• PFam- a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs). www.sanger.ac.uk/Software/Pfam

• RFam- a collection of RNA families, each represented by multiple sequence alignments, consensus secondary structures and covariance models (CMs). www.sanger.ac.uk/Software/Rfam

• miRBase- a searchable database of published miRNA sequences and annotation. microrna.sanger.ac.uk

Other Resources

• Textpresso- a text-mining system for scientific literature. www.textpresso.org

• NCBI Tools for Data Mining-  www.ncbi.nlm.nih.gov/Tools

• Toolbox at the EBI- provides a comprehensive range of tools for the field of bioinformatics. www.ebi.ac.uk/Tools

• ExPASy Proteomics Tools- www.expasy.org/tool

• EM Data Analysis Software- tool for manual abstraction of anatomical features into graphs.www.physics.ucsd.edu/~pb/public_html/software.html