Comparative Genomics
The Analysis Engine offers two different methods for doing comparative analysis of prokaryotic genomes:

• The first method employs protein clustering using Jaccard filtered bi-directional best blast matches. This method does not employ whole genome alignment, but rather compares genomes based on their proteins by building ortholog clusters. Since this method relies on protein, not DNA, sequence to build the clusters, the genomes can be fairly unrelated in this analysis.
• The second method employs the Mugsy genome alignment algorithm. This method does not require a reference and builds protein ortholog groups based on nucleotide alignments and synteny thus helping to differentiate between paralogs and orthologs. However, this method requires that the genomes being compared be fairly closely related.

For both comparative methods, the tool Sybil is used to visualize the results. Sybil is a web-based graphical user interface that allows users to search and view ortholog clusters, genomic context, synteny, and much more. Users are given password-protected access to their results loaded into a Sybil instance as part of the service.

Depending on the goals of your project and the genomes to be included in the analysis, IGS Analysis Engine staff will help you determine which method to use for your data. To discuss the specific needs of your project please contact us.

Training workshops are available on this topic.

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