An Introduction to GAEVAL: A Tool for Gene Annotation Evaluation

These pages serve as both a detailed description of GAEVAL output and as a guide to those wanting to download and implement it locally.
Included in the GAEVAL package are example annotations and evidence alignments provided in GFF3 format.
Each example is included to highlight features of the GAEVAL algorithm and considerations for 'real-world' application.
Detailed descriptions of each example as well as highlights of the GAEVAL output for each are available using the links on the left side of these pages.
Links to additional documents describing GAEVAL features are also found to the left.

GAEVAL Workflow:

Downloading and configuring GAEVAL

Individual examples can be run using the following command line format.

% perl --clean_db --GFF examples/example#.gff3

Example 1: Single Annotation with Evidence (the simple life)

This example introduces the basic report capabilities of GAEVAL including a summary of each analyzed annotation showing genomic source, structure, ORF, 5'UTR, CDS, 3'UTR. Each GAEVAL report also includes a 'Structure Analysis' section detailing the support for the given annotation structure based on supplied evidence alignments. Also available in each GAEVAL report is an 'Incongruency Analysis' section describing possible sources of incongruence between the annotation and given evidence alignments.

Example 2: Erroneously Overlaping Annotations

This example illustrates a very specific form of incongruence in which an automated annotation process has erroneously extended an annotation structure through the ambiguous inclusion of an evidence alignment in multiple adjacent gene structures.

Example 3: Alternative Splicing

This example illustrates the use of GAEVAL in evaluating alternative splicing. In addition to the standard evaluation of observed incongruent introns, this example also showcases the ability of GAEVAL to determine if an incongruent structure has previously been documented by an alternatively spliced isoform (alternative transcript of the evaluated annotation)

Example 4: Alternative Transcript Termination

This example illustrates the ability of GAEVAL to determine the presence of alternative cleavage/polyadenylation site usage based on the clustering of end defining evidence such as three-prime EST alignments.

Example 5: Annotation Fission / Split

This example illustrates the ability of GAEVAL to detect evidence suggesting that an annotation be split into two individual annotations.

Example 6: Annotation Fusion / Merger

This example illustrates the ability of GAEVAL to detect evidence suggesting the merger of adjacent annotations.

Example 7: Pseudo-Introns

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.