MSOAR 2.0: Incorporating tandem duplications into ortholog assignment based on genome rearrangement

BMC Bioinformatics

Table 3 Differences between the ortholog pairs assigned by MSOAR 2.0 and those by the other programs.

Pair of Species	MSOAR 2.0 vs InParanoid		MSOAR 2.0 vs Ensembl		MSOAR 2.0 vs MSOAR
	TPs in MSOAR 2.0 but not in InParanoid ^a	Not BBHs ^b	FPs in Ensembl but not in MSOAR 2.0 ^c	Inparalogs in TAGs ^d	FPs in MSOAR but not in MSOAR 2.0 ^e	Inparalogs in TAGs ^f
human vs mouse	487	408	2,997	2,664	330	312
human vs rat	429	400	2,681	2,366	311	299

(a) This column lists the number of TPs found by MSOAR 2.0 but missed by InParanoid. (b) This column lists the number of TPs in the previous column that are not BBHs. (c) This column lists the number of FPs found by Ensembl but not by MSOAR 2.0. (d) This column lists the number of FPs in the previous column that are inparalogs occurring in TAGs. (e) This column lists the number of FPs found by MSOAR but not by MSOAR 2.0. (f) This column lists the number of FPs in the previous column that are inparalogs occurring in TAGs.

ISSN: 1471-2105