Help with WormMine and Custom Queries

Hello all - I am hoping to use Wormmine on a list of genes I have to quickly identify those that have any alleles or mutations (Classical or change of function). I read the user guide and cannot really understand how to constraint to the list (i.e. I am unable to find the list constraint for the lists I have created).

Help is appreciated !

Hi - I actually figured out how to constrain to a list of genes. Need help trying to figure out how to locate all genes within the list that have either a classical allele or a reference allele.


You can constrain your query to a list of genes in the gene constrain dialog box. Click on the checkbox underneath the main constraint entry box, to the right of “OR” and left of “Contained in list:” and then select you gene list from the available lists of genes provided in the drop down menu. WormMine doesn’t have the allele attributes that distinguish alleles as “classical” or “change of function”, but we can apply other filters such as omitting any Million Mutation Project alleles or those identified by whole genome sequencing (WGS). Here’s a screen recording video showing how this can all be done:

Please let me know if you have any trouble or have any questions.


You can import the following query to see how to constrain to genes that have a reference allele:

[font=arial]“Reference Allele” is actually a separate attribute of genes in WormMine and can be constrained to “have a value”. As I mentioned in my earlier post, WormMine does not classify alleles as “classical” so you’ll have to filter by one of the other attributes available.