Automated alignment-based curation of gene models in filamentous fungi

BMC Bioinformatics

Table 1 Benchmarking of the ABFGP performance on validated genes compared to GeneMark-ES

Species		10 pooled species¹	Magnaporthe oryzae ²		Fusarium verticillioides
Method		ABFGP	ABFGP	GeneMark-ES	ABFGP	GeneMark-ES
# unigenes		6,965	956	169	1154	327
Intron	Sn	91.16	91.5	89.3	92.2	90.7
	Pr	97.08	97.4	90.5	98.2	94.3
Exon	Sn	88.54	89.1	88.0	90.4	85.4
	Pr	98.91	99.4	89.1	98.9	87.9
Nucleotide	Sn	98.75	98.3	98.2	99.3	98.8
	Pr	99.08	99.3	97.1	99.0	97.1
Gene³	Sn	79.4 (5,533)	81.7 (781)	n.a.	82.1 (947)	n.a.

Sensitivity (Sn) and precision (Pr) of the gene model components (introns, exons, nucleotides) are expressed in percentages. Sn is calculated as true positives divided by: (true positives + false negatives); and Pr as true positives divide by: (true positives + false positives) [3].
¹A list of all ten fungal species and results per species are provided in Additional file 4.
²Formerly named Magnaporthe grisea.
³The gene sensitivity is the percentage of gene models that is predicted without a single error. Total number of correctly predicted gene models is indicated in between brackets. Gene sensitivity was not provided for GeneMark-ES.

ISSN: 1471-2105