Genome Project Solutions

Version 3 is now available of our evolutionary analysis of the complete genomes of oomycetes and diatoms. This now adds the genome of Pythium ultimum to that of the four previously included oomycete genomes (Phytophthora sojae, P. ramorum, P. infestans, and Hyaloperonospora arabidopsidis) and two diatoms (Thalassiosira pseudonana and Phaeodactylum tricornutum).

At this release, we are analyzing 109,682 total genes. We use a unique, graph-based method to cluster genes into families while considering the evolutionary relationships among the organisms, and then perform a true phylogenetic analysis on each set of genes. We assign all orthologous and paralogous relationships and determine when each gene duplication or loss occurred.

Users can see the multiple sequence alignments and phylogenetic trees of all genes, compare intron-exon structures, and see maps of the relative arrangements of homologous genes across all genomes.
This is part of the PHRINGE (Phylogenetic Resources for the Interpretation of Genomes) method developed by Genome Project Solutions.

Learn more about the methods used here.

Results can be seen here.

In addition, this version includes many updates to the process and presentation, including rewriting nearly all of the code for greater efficiency, changing dependencies from identity scores to distance scores, which can be calculated in a more sophisticated way, and refining of the way that alignment gaps are handled and colinearity of homologous genes is presente

The initial development of PHRINGE was created as part of the project "Phytophthora sojae: A High Quality Reference Sequence for the Oomycetes", directed by Brett Tyler of the Virginia Bioinformatics Institute, and funded by the U.S. National Science Foundation / U.S. Department of Agriculture Microbial Genome Sequencing Program.

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