GAEVAL uses the analysis of introns both to determine the support for a given annotation and to explain inconsistencies between annotation structures and evidence alignments. Inconsistencies such as alternative splicing are further descibed by GAEVAL using the following incongruent intron flags. GAEVAL extends each flag with a 'documented' property which helps to distinguish novel incongruencies from those already documented in the current annotation collection.
The 'Alternatively Annotated Intron' flag is given to an intron defined by the given annotation which is not found in other available annotation isoforms. Annotation isoforms are considered to be all other annotations in the current annotation set which share at least one common intron with the current annotation or overlap the current annotation by at least one-thousand bases. The 'documented' property of this flag is set when the intron is supported by an isoform specific evidence (ISE) alignment.
The 'Alternative Intron' flag is given to an intron defined by an ISE alignment which is not present in the current annotation and is within the boundaries of the current annotation. The 'documented' property of this flag is set when this intron is present in the structure of one or more annotation isoforms as defined above.
The 'Additional Intron' flag is given to an intron defined by an ISE alignment which is not present in the current annotation yet is also outside the boundaries of the current annotation. The 'documented' property of this flag is set when this intron is present in the structure of one or more annotation isoforms as defined above.
The 'Conflicting Intron' flag is given to an intron defined by the given annotation which is inconsistent with a cognate ISE alignment. The 'documented' property of this flag is set when this intron is present in the structure of one or more annotation isoforms as defined above.
The 'Pseudo-Intron' flag is given to an intron defined by the given annotation which is inconsistent with a cognate ISE alignment and is supported by a noncognate evidence alignment. The 'documented' property is not used for this flag.