Hey UGENE community,

I am a student enrolled in an upper level Bioinformatics course at a university in the US. I am currently working on a final project and am seeking guidance from people in the community. After aligning a few thousand genes (actually 600 bp upstream flanks of protein coding genes of saccharomyces cerevisiae from BioMart), I want to show if closely related promoter regions are consistent among similarly functioning proteins, in other words, if large clades of the generated tree associate with proteins of similar functions, such as all ion transport proteins share similar promoter sequences, etc. To do this, I want to be able to generate a tree that distinguishes specific regions based on information that was inputed along with a gene name and sequence. So a final product would a be a tree (likely circular) that is colored to show how the different gene promoters in question's differ in function. This may require some rules, such as genes with a function labeled as "ion_transport" will be colored red. A visual assessment of similar regions can then be conducted and potential consensus sequences of similar proteins can be generated.

This project is due within a week, so a prompt response would be greatly appreciated.

Thanks,
K