Basidiomycete Genomics

We are currently conducting searches of the genomes of Phanerochaete chrysosporium and Coprinus cinereus for putative genes coding for particular groups of enzymes. One area of interest is proteases, as we are also looking at secreted protease enzyme activity in Coprinus. Another area is degradative enzymes that might have value in bioremediation. In both projects, we're using HMMer to search for conserved domains specific to particular protein families, then attempting to characterize complete genes from the genomic DNA.

As part of this project, we have developed a "genome excerpter" that will locate a particular segment of interest from a scaffold in either genome under study, return the DNA sequence of the segment, translate it in all reading frames, align those reading frames with the DNA sequence, and locate possible 5' intron junctions and branch points in the segment. All of these are options in the program hmm3.pl.

We have also translated the genomes of Phanerochaete chrysosporium and Coprinus cinereus in all reading frames, and the translations can be searched using Blastp or blastx on our site.