SwissProt PropertyComparison HowTo
A SwissProt PropertyComparison object is able to compare the following properties of two SwissProt Input objects
- EC (Enzyme Comission) numbers
- OG (Organelle)
- OS (Organism Species)
- OC (Organism Classification)
- RX (MEDLINE and PubMed IDs)
- KW (Keywords)
- FT (Feature Table) key names
- DR (Domain information)
In order to conduct the comparison select your SwissProt Input objects and click on
SwissProt -> PropertyComparison (see picture below).

All entries of each property contained in the SwissProt objects are compared to calculate absolute and relative
frequencies as well as ratios of these fequencies between the two SwissProt objects.
absolute frequency
Specifies the number of occurrences of a property entry in its SwissProt object.
relative frequency
Specifies the number of occurrences of a property entry in its SwissProt object, relative to the total
amount of entries of this property.
absolute ratio
The ratio is calculated by dividing the smaller absolute frequency value of a property entry by the
greater absolute frequency value.
The result is a value between 0 and 1 wich describes the similarity of the occurrence of this property entry between
the two SwissProt objects.
The closer to 1 the value is, the property entry, focused on, appears in both SwissProt objects relatively
similar.
The amount of appearences of this property entry is equal in both SwissProt objects, if the value equals 1.
The closer to 0 the value is, the property entry, focused on, appears in both SwissProt objects relatively
dissimilar.
If the absolute frequency value of one property entry of an SwissProt object equals 0, the absolute ratio is set to
-Infinity to express maximum frequency difference.
relative ratio
The calculation equals that of the absolute ratio but instead of absolute frequency values, relative frequencies are
used.
log ratio:
The log ratio value is calculated by logarithmizing the relative ratios between SwissProt objects.
Some settings have to be done before running the PropertyComparison Engine affecting the output using the data viewer
or visualisation option.
More precisely, the following user-defined parameters must be satisfied by the properties of the SwissProt objects to
be displayed in the data viewer or depicted in the resulting barchart
- kBest
- abundance
- maxRelRatio
- minRelRatio
kBest
Specify the maximum number of results that shall be displayed (disable to show all results). The k best entries will
be chosen depending on the sorting type selected. The value must be an integer greater than 0.
abundance
The minimum relative frequency (a real number in the range of 0 and 1) that has to be satisfied of the accumulated
absolute frequencies of an property entry in both SwissProt objects with respect to the number of property entries in
both SwissProt objects.
In detail, the formula

has to be true.
maxRelRatio
The maximum relative frequency ratio (a real number in the range of 0 and 1) has to be satisfied.
In detail, the formula

has to be true.
minRelRatio
The minimum relative frequency (a real number in the range of 0 an 1) that has to be satisfied of an property entry in
one SwissProt object if the relative frequency of the corresponding property entry in the other SwissProt object equals
0 (and therefore no meaningful ratios can be calculated).
In detail, the formula

has to be true.
As a last setting, the option sort by defines which value to be used to sort the results in the data viewer.