A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach

BMC Bioinformatics

Table 2 Comparison of intron structure predictions in S. cerevisiae and N. castellii by YGAP and AUGUSTUS

Species	Software	Predicted introns (a+b+c)	False positives (a)	Completely correct (b)	Real intron, incorrect coordinates (c)	False negatives (d)	Total introns studied (b+c+d)
S. cerevisiae	YGAP	146	2	127	17	122	266
	AUGUSTUS	221	90	87	44	121	252
N. castellii	YGAP	146	12	123	11	58	192
	AUGUSTUS	251	173	58	20	94	172

Note that False Negatives in YGAP include not only those genes for which no intron was predicted by the software, but also those for which intron coordinates could not be defined and were tagged for manual curation. The total number of introns studied (rightmost column) differs between YGAP and AUGUSTUS because some genes were not predicted by both methods.

ISSN: 1471-2105