Example 5: Annotation Fission / Split

perl xGAEVAL.pl --clean_db --GFF examples/example5.gff3

Description:

This example illustrates the ability of GAEVAL to detect evidence suggesting that an annotation be split into two individual annotations. In this example, the Arabidopsis gene locus ( At1g07620.1 ) should most likely be split into two individual gene annotations.

GAEVAL Results:

Incongruency Analysis (At1g07620.1)

1:  Putative 'Fission' site detected:
2:   2344461
3:    Supporting Evidence: 2
    

Fission sites are detected by first finding an alternative cleavage / polyadenylation site as in example 4. If no evidence suggest transcription through one of these sites, a fission event is considered possible.

• line 1: GAEVAL has detected a putative 'Fission' event
• line 2: Location of each fission event
• line 3: Count of end-defining evidence supporting this fission event

Discussion:

In this example a full-length cDNA sequence (gi number 51968419) and a three-prime EST (gi number 40452728) establish a 'Three-Prime Evidence Group'. This cleavage/polyA site is exceptional far from the annotated terminus. In addition, no evidence alignments were found to align across this site. These factors provide GAEVAL the neccessary criteria to consider this a 'fission' event.