In the first phase, more than 2.8 million predicted protein coding genes, from 3,774 organisms, including viruses, were added to the database for a ALL against ALL comparison. These include more than 400 complete genomes. Sequences were grouped in blocks of 2000 sequences each, and more that 1 million block to block comparisons are planned. With an average redundancy of about 3x, 3 million block comparisons are scheduled for this phase.

The current phase is only the first step in our Genome Comparison project, since the next step may be the comparison of genomic regions that have the potential to be coding, but are currently not recognized as such, which may be due to the algorithms used for gene prediction, among other factors.