This page is designed to help you in the choice of your query and groups of species of interest.
The selection of your query depends both on the proteins you want to work with, and the species you want to compare. If you wish to work with human proteins, you should select Homo sapiens as your reference species, likewise, if you want to work with Arabidopsis thaliana proteins, your should select it as your reference. The query species should be in the same life domain as the species you want to study, and should be distant enough from these to allow for accurate results (see below).
Blur detects differential conservation at both the gene and the sub-gene level by perfoming relative comparisons between two groups of species. This allows for the comparison of species that are quite close, as well as species that are more distant. The only important criteria is that the two groups of species you want to compare should have diverged more recently that either of them did with the reference species you have chosen . For better results, groups of interest should contain at least 3 species.
For the comparison of two groups with no previous knowledge , we recommend selecting a query species that is as close to your two groups of species' common ancestor as possible, to allow for a finer analysis.
For the study of genotype/phenotype correlation , we recommend selecting a query species and a group of species that share your phenotype of interest, and compare the latter to a close group of species in which the phenotype is absent. To help with this choice, BLUR is able to suggest sister clades to your group of interest.
In the example provided on the BLUR homepage, ciliated Fungi (Chytridiomycota, Blastocladiales and Rozella) are compared to non ciliated Fungi (Dikarya). The reference species selected should thus be more evolutionary distant to either group than the groups are together, and should present the phenotype of interest, in this case, cilia. Hence, we chose Homo sapiens.