Automated alignment-based curation of gene models in filamentous fungi

BMC Bioinformatics

Table 3 Introspection of results obtained by the ABFGP method

Species	Botrytis cinerea		Cladosporium fulvum		Dothistroma septosporum		Mycosphaerella fijiensis		Verticillium dahliae		Zymoseptoria tritici ¹		Pooled unigenes²
Total number of assessed genes³	8,337		7,547		8,019		7,231		8,260		7,815		6,965
Confirmed/unchanged	4,832		5,823		6,249		4,775		5,390		5,262		Correct
Labeled ‘ok’⁴	3,942	82%	5,186	89%	5,505	88%	4,216	88%	4,536	84%	4,539	84%	5,015 (TP)
Labeled ‘doubtful’⁴	890	16%	637	11%	744	12%	559	12%	854	16%	723	16%	533 (FN)
Revised	3,505		1,724		1,770		2,456		2,870		2,553		Incorrect
Labeled ‘ok’⁴	2,137	61%	1,160	67%	1,209	68%	1,730	70%	1,864	65%	1,734	68%	899 (FP)
Labeled ‘doubtful’⁴	1,368	29%	564	33%	561	32%	726	30%	1,006	35%	819	32%	496 (TN)

¹Formerly named Mycosphaerella graminicola.
²Correctly predicted gene models (benchmarked on the full-length unigenes) that were labelled by the introspection procedure as ‘ok’ are true positives (TP) and labelled ‘doubtful’ are false negatives (FN). Genes that were incorrectly predicted and were labelled ‘ok’ are false positives (FP) and labelled ‘doubtful’ are true negatives (TN).
³Total eligible number of genes minus number of genes aborted during execution (Table 2).
⁴Number and percentage of genes that are labelled ‘ok’ and ‘doubtful’ by the introspection procedure in each category.

ISSN: 1471-2105