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## Uses of Class
de.jstacs.data.sequences.annotation.MotifAnnotation

Packages that use MotifAnnotation
de.jstacs.data.sequences.annotation | Provides the facilities to annotate `Sequence`s using a number of pre-defined annotation types, or additional implementations of the `SequenceAnnotation` class
de.jstacs.motifDiscovery | This package provides the framework including the interface for any de novo motif discoverer

Uses of MotifAnnotation in de.jstacs.data.sequences.annotation

Constructors in de.jstacs.data.sequences.annotation with parameters of type MotifAnnotation
`CisRegulatoryModuleAnnotation(String identifier, MotifAnnotation[] motifs, Result... additionalAnnotation)` Creates a new `CisRegulatoryModuleAnnotation` from a set of motifs and possibly additional annotations.

Uses of MotifAnnotation in de.jstacs.motifDiscovery

Methods in de.jstacs.motifDiscovery that return MotifAnnotation
`MotifAnnotation[]` | `SignificantMotifOccurrencesFinder.findSignificantMotifOccurrences(int motif, Sequence seq, int start)` This method finds the significant motif occurrences in the sequence.
`MotifAnnotation[]` | `SignificantMotifOccurrencesFinder.findSignificantMotifOccurrences(int motif, Sequence seq, int addMax, int start)` This method finds the significant motif occurrences in the sequence.

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