Description of the genome query for

Comparative inventories: Pairwise comparison

For each ORF in the first chosen genome, and for each of the ORF's matches to the database that is better than or equal to the specified BLASTP cutoff e-value, a check is made to see if the hit is to a sequence from the second genome.

If any are, the ORF is reported if the user selected "are found".

If none are, the ORF is reported if the user selected "are not found".

Examples:

1. A good reason for sequencing closely-related strains of bacteria is to try to understand what makes them phenotypically different. This is especially interesting when comparing pathogens, which might have different degrees of virulence, different host specificities, etc. On March 22, 2000, the pair of most closely-related genomes in the public databases are those from strains of Chlamydia pneumoniae (C. pneumoniae CWL029 and C. pneumoniae AR39, the latter annotated as Chlamydophila pneumoniae). Despite their marked sequence and genomic similarities (see organismal phylogenies, and genomic dot plots in order to be convinced), C. pneumoniae CWL029 possesses 108 ORFs not present in C. pneumoniae AR39; conversely, C. pneumoniae AR39 possesses 77 ORFs not present in C. pneumoniae CWL029. These results were obtained by selecting a very low stringency for matching (BLASTP cutoff e-value of 1.0e-5), selecting the two genomes from the pop-up menus, and selecting "ORFs from Genome #1 which are not found in Genome #2".
2. Referring to example 1 above, since some of the differences may simply be differences (errors?) in annotation, one can first filter the genome through the "non-organism-specific ORF" query, then use the results from this query as the input to the comparative genomics query being discussed here. Doing so gives the following results: CWL029 retains 97 ORFs not present in AR39; and AR39 still retains 77 ORFs not present in CWL029. These ORFs should be the first ones characterized experimentally if one is to understand the biological differences between these two chlamydiae.

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