- What is BlastO?

- How are the ortholog groups identified?

- How trustful are the phylogenetic trees constructed using ClustalW from this site?


- What is BlastO?

BlastO is a modified Blast designed for searching ortholog group data. It treats each ortholog group as a unit, and organizes and ranks the BLAST results by ortholog groups instead a ranked list of individual sequence hits.
For each query sequence, BlastO performs BLAST on the complete genome data from each species in COD. The result from a BlastO search includes three parts. The first part is a ranked list of ortholog groups that contains genes that share significant similarity with the query sequence. The score of each ortholog group is computed as the average score among all the ortholog genes within that group (i.e. the sum of scores from all the orthologs in the group divided by the number of orthologs in that group). The second part is the separate ranked list of genes in each species that are not contained in any ortholog groups. The third part, as other BLAST family programs, displays the alignments of the query sequence with each individual sequences. An example of BlastO output is displayed below.



- How are the ortholog groups identified?

The ortholog groups between the currently available two ciliate genomes are identified using Inparanoid program. Inparanoid program uses reciprocal best hits as the anchor for each ortholog group and further expand the group to include in-paralogs (ortholog genes that are duplicated after speciation). In-paralogs are identified as genes that are more similar to some genes within the same genome that are already included in an ortholog group than any genes in any other species. For more detail, please see the Inparanoid paper.

- How trustful are the phylogenetic trees constructed using ClustalW from this site?

The ClustalW program on our database site runs under default settings (automatic identification of DNA or Protein type; DNA weight matrix: IUB, Protein weight matrix Gonnet; phylogenetic tree construction: Neighbour Joining method of Saitou and Nei). It is provided for users to get a preliminary sense of the data in a fast and easy way. For further analysis, one may consider alternative parameter settings or more sophisticated phylogenetic programs.