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Figure 10 | Genome Biology

Figure 10

From: Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Figure 10

Addition of alternatively spliced isoforms using PASAu. By applying Program to Assemble Spliced Alignments (PASA) to the various annotation datasets, PASA can automatically annotate alternative splicing isoforms. The number of alternatively spliced genes and the number of transcripts per alternatively spliced gene are shown, including the pre-PASAu and post-PASAu values. Only the EnsEMBL dataset includes models for alternatively spliced isoforms before the application of PASA. Dotted lines indicate the corresponding values based on the GENCODE reference annotation dataset: 147 alternatively spliced genes and 3.42 transcripts per alternatively spliced gene. Transcript isoforms alternatively spliced only in untranslated regions were ignored. Here, EVM:All(+OP) refers to the inclusion of the EVM:All evidence plus the 'other predictions' from ENCODE Genome Annotation Assessment Project (EGASP), including EnsEMBL, ENSgene, KnownGene, and CCDSgene, used by EVidenceModeler (EVM) as the OTHER_PREDICTION evidence class (Table 1).

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