A Gegenees primer mapping compares one or several short sequences with one or several genomes and presents the results in a table.
In the menu bar, click "New" -> "New primer mapping..." and a dialog will apear. Here you should select a name for your primer mapping and add short sequences in fasta format to the text box.
It i possible to either type in the short sequences, copy-paste them or load directly from a fasta file on the filesystem, and click next. In this screenshot there is one sequence from the chromosome of the Bacillus anthrasis Ames Ancestor strain. One sequence from the Bacillus anthrasis plasmid PXO2 and one from the plasmid PXO1, which both are precent in all Barcillus anthrasis species, but non existent in most of the Bacillus cereus species.
Then add genomes from the local database to the list of included genomes by selecting them and then clicking on the right arrow (">"). Here, two Bacillus anthrasis strains and three Bacillus cereus strains are chosen. Then click "Finish" followed by "Start".
The primer score table presents the results of the primer mapping in a tabular form. The table displays sequence identity, query length, alignment lenght, missmatches, gaps and the unalignment index. The unalignment index is designed in such a way that it shoud be easy to spot a perfect sequence match. The index is calculated as gaps + mismatches + query length - (alignent length - gaps), so a zero in the unalignment index column means a perfect hit.
In this screenshot, all primers have a perfect hit against the Ames Anscestor strain and the Vollum strain, but the there is disparity between all primers and the cereus strains.
If the tabular information is not enough, it is also possbile to view the raw BLAST result in a separate window by clicking the button in the top right corner named "Show alignment".
It is also possible to load a grouping from a previously analysed fragmented all-all comparison. Click the "Load grouping from comparison"-button and select a comparison and then a grouping from that comparison.
Here we can se that our primers can discriminate between target group and background group.