FEDRO: a software tool for the automatic discovery of candidate ORFs in plants with c →u RNA editing

BMC Bioinformatics

Table 4 Putative ORFs resulting from Tblastn query for EST sequence similarity search obtained for O. sativaFEDRO ORFs

seq	start	stop	strand	start	orf	orf	blastp	similarity found
nr.	type	type	type	codon	length	type	bitscore	organism
2	Edited	Main	rev	105822	306	New	195	O. longistaminata
3	Main	Edited	rev	444521	354	Sub	194	O. sativa Japonica Group
4	Edited	Edited	rev	444885	411	New	194	O. sativa
5	Edited	Main	rev	55809	378	Sub	179	O. punctata
6	Main	Main	fwd	250268	342	Sub	171	B. oldhamii
7	Edited	Edited	fwd	407800	318	New	167	P. virgatum
8	Edited	Edited	fwd	354085	357	New	159	O. longistaminata
9	Edited	Edited	fwd	362648	315	New	145	F. pratensis
10	Edited	Edited	rev	449361	327	New	142	T. cacao
11	Edited	Edited	rev	295218	324	New	114	V. vinifera
12	Edited	Main	rev	207984	306	New	112	O. sativa Japonica Group
13	Edited	Main	fwd	385977	318	New	91	S. officinarum
14	Edited	Main	rev	248349	318	New	89	O. sativa Indica Group
15	Edited	Edited	fwd	203320	375	New	85	T. cacao

Best hit bitscore and organism where the significant sequence similarity has been found are reported for each ORF. This table contains sequence similarity results corresponding to BLAST bitscore in the range 80−200

ISSN: 1471-2105