Constraint Elements

To add a constraint element, add the required algorithm elements to the scene and drag & drop the necessary constraint element.

When a constraint element is added, two algorithm elements are selected.

There are four types of constraints that you can impose on the positional relationship of the results obtained from algorithm calculations: End-Start, Start-End, End-End, and Start-Start.

In the image below, you can see a schema with Pattern and ORF algorithm elements and an End-Start constraint:

This means the following:

  1. The algorithm elements specify the analysis of the sequence with Pattern and ORF algorithms. The results of these analyses are sets of annotations.

  2. The condition states that the distance between a “Pattern annotation end” and an “ORF annotation start” should be within the specified bounds, i.e.:

Let:

  • pattern_annot_end := the last nucleotide of an annotation obtained from the Pattern algorithm calculations
  • orf_annot_start := the first nucleotide of an annotation obtained from the ORF algorithm calculations

The constraint is:

0bp <= Distance(pattern_annot_end, orf_annot_start) <= 100bp

Find the details on each constraint element below.

« HMM2 Algorithm Element End-Start Constraint Element »