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Genotype management

Did you forget to add genes to the session or you want to remove some?

In the main menu, click on Edit gene list on the right side of the interface.

  • To remove genes, tick the boxes on the right, then click Remove selected. You can only delete genes that have not been used for annotations.
  • To add genes, click Add more genes from ....
    • You can add multiple genes separated by any spacer (space, commas, line breaks).
    • You can refer to genes by their systematic id (SPAC3G9.12), primary name (peg1) or a synonym (cls1).
    • If a gene name is also the synonym of another gene (e.g. psu1), you will be asked to provide a primary name for that gene.

Video summary

Creating genotypes

On the left side of the session page, click on Genotype management. This will take you to a screen where you can see all the genes you have added to the session.

Creating single-locus genotypes

  • To create a genotype with a deletion allele, click on Deletion.
  • To create a genotype where the expression level of the wild-type allele is altered (e.g. overexpression), click on Other Genotype and select wild type as allele type. Then select the expression level.
  • For others, click on Other Genotype, then:
    • First, check if the allele you want to use already exist by writing its name on the Allele name text box. If you find it, click on it, and the allele details will be imported from PomBase.
    • Otherwise, create a new allele:
      • Give it the name that it has in the publication. Ideally, the name should follow our guidelines.
      • Select the type of allele, and add an allele description following the displayed example. See all description examples.
    • Finally, select the expression level and click OK.

Creating diploid loci

  • If you want to make a diploid genotype with two different alleles, they must exist as separate single-locus genotypes.
  • Start from a haploid single-locus genotype that contains one of the desired alleles, and tick the box on its left.
  • Then, click on Create diploid locus, there you can choose to create either:
    • An homozygous locus with the starting allele.
    • An heterozygous locus with the starting allele and the wild-type.
    • An heterozygous locus with the starting allele and another allele from the session (choose from the dropdown).
  • Then click OK.

Creating multi-locus genotypes

  • Select all single-locus genotypes that you want to combine in a multi-locus genotype, by ticking the boxes on their left.
  • Click the button Combine selected genotypes.
  • You can also create diploid multi-locus genotypes by combining diploid single-locus genotypes.

These are just the basics, more info and edge cases can be found in the FAQs