LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

BMC Bioinformatics

Table 3 List of clusters of LTRharvest predictions compared to the Drosophila melanogaster annotation

LTR retrotransposon predictions from *LTRharvest* and clustering		*Drosophila melanogaster* annotation of LTR retrotransposon families from [26]
cluster	# sequences in cluster	name of family	full-length sequences	all sequences
LTRharvest_Dmel0	92	Roo	58	146
LTRharvest_Dmel1	18	opus	16	24
LTRharvest_Dmel2	15	mdg1	13	25
LTRharvest_Dmel3	2	McClintock	2	2
LTRharvest_Dmel4	22	blood	22	22
LTRharvest_Dmel5	26	412	24	31
LTRharvest_Dmel6	50	297,17.6	25	69
LTRharvest_Dmel7	12	Stalker, Stalker2, Stalker4	9	27
LTRharvest_Dmel8	3	rover	3	6
LTRharvest_Dmel9	15	micropia, DM88, invader1	3	63
LTRharvest_Dmel10	3	invader3	3	16
LTRharvest_Dmel11	19	Tirant	15	20
LTRharvest_Dmel12	28	copia	26	30
LTRharvest_Dmel13	9	diver	9	9
LTRharvest_Dmel14	6	Quasimodo	5	14
LTRharvest_Dmel15	5	Transpac	5	5
LTRharvest_Dmel16	3	Idefix	2	7
LTRharvest_Dmel17	12	Burdock	7	13
LTRharvest_Dmel18	3
LTRharvest_Dmel19	16	blastopia	13	17
LTRharvest_Dmel20	6	springer	5	11
LTRharvest_Dmel21	12	HMS-Beagle	9	13
LTRharvest_Dmel22	3
LTRharvest_Dmel23	5
LTRharvest_Dmel24	3	GATE	0	20
LTRharvest_Dmel25	8	mdg3	8	16
LTRharvest_Dmel26	4	invader2	3	10
LTRharvest_Dmel27	2
LTRharvest_Dmel28	4	3S18	4	6
LTRharvest_Dmel29	2	gypsy5	1	2
LTRharvest_Dmel30	3
LTRharvest_Dmel31	2
LTRharvest_Dmel32	2	gypsy, gtwin	3	8
LTRharvest_Dmel33	2	invader4	2	9
LTRharvest_Dmel34	2	Tabor	2	3
LTRharvest_Dmel35	2

For clustering the program Vmatch was used with the following options: seedlength for minimal length of exact repeats = 50, minimal length of matches = 2500, Xdrop = 9 and matching conditions (dbcluster) that cover at least 80% of the smaller sequence and 28% of the larger sequence.
Of 49 annotated families [26], this Table lists 34 out of 41 families containing at least one full length member and one family (GATE) out of 8 families that are entirely composed of partial elements.

ISSN: 1471-2105