The databases
mmp strains: the library of 2007 mutagenized C. elegans strains
wild isolates: the set of 40 wild isolates
Search for C. elegans genes
Mutations were mapped to Wormbase release 230. You can either use CGC gene names (e.g. unc-52) or sequence names (e.g. F15B9.7) as identifiers. You cannot search directly for mutations is particular splice variants. Do not use splice variant designations or other identifiers in this search field.
Protein domains
SMART was used to identify protein domains in C. elegans proteins. SNVs affecting coding exons were mapped to the amino acid affected. If the affected amino acid is in a known protein domain, the domain will be shown in the output table. You can limit the output to mutations affecting only particular domains. Note that you can also search for mutations in particular protein domains without specifying a list of genes.
Chromosomal regions
You can search for mutations in genomic regions of interest such as putative promoter regions by specifying a genomic interval. Make sure you have checked the relevant checkboxes on the right to ensure that the correct type of mutation is shown (e.g. check the box "intergenic" when searching for mutations in intergenic regions).
Strains
You can find all mutations in a particular strain by entering the strain name in this search field. Specify the chromosomal region (see above) to only show mutations in a particular genomic interval in a strain. Output is limited to the types of mutations selected with the checkboxes on the right side. Make sure that all checkboxes are checked, if you want to see all mutations in a strain.
Plots
A genome-wide visualization of copy number variants and heterozygous sites is also available through the "plot" link next to the strain name in the search results. The top figure shows regions of significantly increased or decreased coverage with red dots. The bottom figure plots the fraction of aligned bases disagreeing with the reference sequence for SNVs, with red dots denoting possible heterozygous sites. Clusters of such sites are present in some strains.
Types of mutations
Output is always limited to the types of mutations selected by the checkboxes on the right. The overwhelming majority of the mutations are Single Nucleotide Variations ("SNVs"), but some are deletions and/or insertions ("indels"). Mutations are categorized depending on whether they affect "exons", "introns", "UTRs" or "intergenic" regions. Mutations affecting exons are further subdivided into those leading to stop codons ("nonsense") or amino acid changes ("missense"). Additional categories are silent mutations ("synonymous"), mutations affecting the start codon ("start ATG") or the stop codon ("readthrough") and mutations affecting either splice donors or acceptors ("splicing"). Since indels can have more complex consequences they are kept as separate category. Mutations affecting non-coding RNAs are subdivided into mutations affecting transfer RNAs ("tRNAs"), ribosomal RNAs ("rRNAs"), small nuclear RNAs ("snRNAs"), small nucleolar RNAs ("snoRNAs"), small cytoplasmic RNAs ("scRNAs"), Piwi-interacting RNAs ("piRNAs") and micro RNAs ("miRNAs").
C. elegans homologs of human genes
Human homologs of C. elegans genes were identified ...
You can use Ensembl gene identifiers (Ensembl release v65) in this search field to identify the corresponding C. elegans homolog(s) and mutations in them.
Output options
Use "web page", if you want to view the search results in your web browser. Use "text only" for a tab-delimited text-based output that can be saved and further processed locally. You can sort the output in various ways using the "sort by" options. You can collapse identical mutations found in different strains into one row. Display of Grantham and conservation scores (GERP++, phyloP, phastCons) is optional. A list of restriction enzymes allowing you to distinguish between the reference sequence (ref) and the mutation (mut) can be shown as well. Ensembl IDs are shown by default only, if they were used as search terms. For other types of searches the display of Ensembl IDs (of human homologs!) is optional.
Combinatorial searches
Combinatorial searches can be done by entering search criteria in more than one search field. Only records fulfilling all search criteria will be shown. Output is always limited to the type of mutations specified by the checkboxes on the right side. Make sure you don't leave text in search fields inadvertently and check the appropriate boxes for the type of mutation you are looking for.