SLIDR and SLOPPR: flexible identification of spliced leader trans-splicing and prediction of eukaryotic operons from RNA-Seq data

Table 1 Comparison of SLs and SL RNA genes detected by SLIDR and SLFinder in four eukaryotes (Caenorhabditis elegans, Ciona intestinalis, Hydra vulgaris and Schistosoma mansoni)

Species	SL	Pipeline	SL sequence	SLs detected	SL RNA genes detected
C. elegans	Cel-SL1	SLIDR	-agtcGGTTTAATTACCCAAGTTTGAG------	100% (1/1)	100% (10/10)
		SLFinder	ggaggGGTTTAATTACCCAAGTTTGAGaaaatg	100% (1/1)	100% (10/10)
			-------------TACCCAAGTTTGAGgtaatc
C. elegans	Cel-SL2	SLIDR	ttGGTTTTAACCCAGTTAACCAAG--- ^a	100% (11/11)	100% (18/18)
		SLFinder	-tGGTTTTAACCCAGTTAACCAAGatg	9% (1/11)	44% (8/18)
C. intestinalis	Cin-SL	SLIDR	taaggcATTCTATTTGAATAAG-	100% (1/1)	73% (11/15) ^b
		SLFinder	----ggATTCTATTTGAATAAGa	100% (1/1)	0% (0/15) ^c
H. vulgaris	Hvu-SL-B1	SLIDR	---cttcggaaaaAAACACATACTGAAACTTTTTAGTCCCTGTGTAATAAG-------- ^a	17% (2/12)	2 ^d
		SLFinder	cccggACGGAAAAAAACACATACTGAAACTTTTTAGTCCCTGTGTAATAAGaaaaaaat	8% (1/12)	239 ^d
			-------------------------------------CCCTGTGTAATAAGcaaaaa--
			-------------------------------------CCCTGTGTAATAAGgtttaa--
			-------------------------------------CCCTGTGTAATAAGtaaaaaa-
			--------------------------------------CCTGTGTAATAAGttttaaa-
			---------ccgatctCACATACTGAAACT-----------------------------
S. mansoni	Sma-SL	SLIDR	ctaaccgtCACGGTTTTACTCTTGTGATTTGTTGCATG---	100% (1/1)	110 ^d
		SLFinder	----ccgtcacgGTTTTACTCTTGTGATTTGTTGCATGata	100% (1/1)	132 ^d

Datasets are detailed in Additional file 1: Table S1 and [34]. For each expected SL, the sequences assembled from the RNA-Seq data are presented as alignments, underlining the expected sequence. Lower-case 5′ bases in the SLIDR sequences denote bases supported by fewer than 50% of reads. Numbers of detected out of expected SLs and SL RNA genes are detailed where available
^aOnly the single SL sequence identical to the SLFinder sequence is presented
^bThe remaining four loci are sequence variants of the SL that are not present in the RNA-Seq libraries
^c28 loci were predicted, but none matched functional copies
^dSL RNA genes are poorly characterised in the reference genome (see main text)

ISSN: 1471-2105