Example 7: Pseudo-Introns

perl xGAEVAL.pl --clean_db --GFF examples/example7.gff3


This example illustrates the ability of GAEVAL to detect annotation structures resulting from the use of noncognate / homologous sequence alignments which are incongruent with cognate evidence alignments. In this example, the Arabidopsis gene locus ( At1g03905.1 ) is annotated with the structure represented by noncognate cDNA evidence instead of the more accurate cognate cDNA alignments.

GAEVAL Results:

Incongruency Analysis (At1g03905.1)

1:  Incongruent Introns Detected:
2:   993631..993704
3:     Alternative Intron
4:      Supporting evidence: 1
5:   993631..994044
6:     Conflicting Intron
7:      Conflicting evidence: 1
8:      Supporting evidence: 0
9:     Erroneous (Pseudo) Intron

For an explanation of the introns categories used in this section see the folowing document on incongruent introns.


In this example the annotated gene structure is taken from the alignment of the noncognate cDNA sequence (gi number 42459253). In the absence of cognate evidence for this region, gene structure established by noncognate / homologous evidence is better than ab-initio prediction alone. However, in this example the pressence of the cognate cDNA (gi number 42472210) establishes an incongruent and contradictory intron. This provides GAEVAL the neccessary criteria to consider this a 'Pseudo-Intron'.