vault RNA

Sequences

• Seed sequences
• Seed alignment
• Known sequences used for evaluating
• Erpin epn file, Erpin parameters -02,02 -add 04 06 02 -pcw 61 -cutoff 21.94

Descriptor 1st iteration

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parms
wc += gu;
descr
h5 (tag='H1', minlen=5, maxlen=6)
ss (tag='S1', minlen=5, maxlen=5, seq="NNNNA")
h5 (tag='H2', minlen=4, maxlen=4, seq="GCTC")
ss (tag='S2', minlen=1, maxlen=1, seq="A")
h5 (tag='H3', minlen=4, maxlen=4, seq="GCGG")
ss (minlen=34, maxlen=90)
ss (tag='S5', minlen=10, maxlen=10, seq="NGTTCGARAC")
h3 (tag='H3')
h3 (tag='H2')
ss (tag='S7', minlen=5, maxlen=5, seq="NNNNN")
h3 (tag='H1')

Descriptor 2nd iteration

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• Diff to desc1
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parms
wc += gu;
descr
h5 (tag='H1', minlen=5, maxlen=6, mispair=1)
ss (tag='S1', minlen=5, maxlen=5, seq="NNNNA")
h5 (tag='H2', minlen=4, maxlen=4, seq="GCTC")
ss (tag='S2', minlen=1, maxlen=1, seq="A")
h5 (tag='H3', minlen=4, maxlen=4, seq="GCGG")
ss (minlen=24, maxlen=100)
ss (tag='S5', minlen=10, maxlen=10, seq="NGTTCGANAC")
h3 (tag='H3')
h3 (tag='H2')
ss (tag='S7', minlen=5, maxlen=5, seq="NNNNN")
h3 (tag='H1')

Descriptor 3rd iteration

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• Diff to desc2
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parms
wc += gu;
descr
h5 (tag='H1', minlen=5, maxlen=6, mispair=1)
ss (tag='S1', minlen=3, maxlen=7)
h5 (tag='H2', minlen=4, maxlen=4, seq="GCTC", mismatch=1)
ss (tag='S2', minlen=0, maxlen=2)
h5 (tag='H3', minlen=4, maxlen=4, seq="GCGG", mismatch=1)
ss (minlen=24, maxlen=100)
ss (tag='S5', minlen=10, maxlen=10, seq="NGTTCGANAC", mismatch=2)
h3 (tag='H3')
h3 (tag='H2')
ss (tag='S7', minlen=3, maxlen=7)
h3 (tag='H1')

Result table

Species	RNAMotif 1	RNAMotif 2	RNAMotif 3	BLAST	Blast Rank	Blast E-Values	ERPIN	ERPIN Rank	RaveNnA	RaveNnA Rank
homo sapiens (3)	3 hits	3 hits	917 hits	31 hits | top hits	(1,2,3)	4e-27 - 1e-23	473 hits	(1,2,3)
pan troglodytes	3 hits	4 hits	813 hits	43 hits | top hits	(1,2,3) new candidates (aln with hom.sap.)	2e-26 - 5e-21	338 hits	(1, 2, 10) cand.
macaca mulatta (3)	2 hits	2 hits	791 hits	32 hits | top hits	(1,2,5)	9e-20 - 0.001	281 hits	(1,2,3)
rattus norvegicus (1)	1 hits	1 hits	1040 hits	61 hits | top hits	(1)	6e-43	104 hits	(1)
mus musculus (1)	1 hits	1 hits	857 hits	44 hits | top hits	(1)	1e-42	177 hits	(1)
bos taurus (1)	1 hits	1 hits	856 hits	59 hits | top hits	(1)	9e-12	294 hits	(1)
canis familiaris (1)			867 hits	43 hits | top hits	(1)	2e-07	883 hits	(1)
monodelphis domestica (1)			936 hits	18 hits | top hits	(1)	0.057	202 hits
ornithorhynchus anatinus (2)			912 hits	159 hits | top hits	(1, 3)	2e-06 - 0.007	74 hits	(1, 3)
gallus gallus (1)			370 hits	55 hits | top hits	(1)	0.001	335 hits
anolis carolinensis			1438 hits	1 hits | top hits	(1) new candidate (aln with xen.tro.)	0.084	55 hits		960 hits
xenopus tropicalis (5)			423 hits	10 hits | top hits	(1, 2, 3, 4, 6)	7e-08 - 0.009	17 hits	(9)	38 hits
danio rerio (4)			282 hits	47 hits | top hits			111 hits		828 hits	(1,2,3,8)
takifugu rubripes (5)			273 hits	12 hits | top hits	(6)	(2.5)	8 hits		318 hits	(1,2,3,5)
branchiostoma floridae (6)			430 hits	1 hits | top hits			5 hits		319 hits	(2,20,52,72,76,81)
ciona intestinalis (2)			66 hits	20 hits | top hits			2 hits		58 hits	(48)
strongylocentrotus purpuratus (3)			277 hits	3 hits | top hits			87 hits		318 hits	(65)
drosophila melanogaster			110 hits	9 hits | top hits			4 hits		57 hits
apis mellifera			182 hits	20 hits | top hits			96 hits		131 hits
caenorhabditis elegans			44 hits	7 hits | top hits			2 hits		84 hits
trichinella spiralis			19 hits	2 hits | top hits			15 hits		131 hits
schmidtea mediterannea			153 hits	3 hits | top hits			187 hits		385 hits
capitella capitata			201 hits	6 hits | top hits			1 hits		63 hits
hydra magnipapillata			1210 hits	108 hits | top hits			15558 hits
nematostella vectensis			276 hits	2 hits | top hits			5 hits		128 hits
trichoplax adhaerens			15 hits	top hits					23 hits
monosiga brevicollis			96 hits	5 hits | top hits					6 hits

The numbers in the "Rank" columns denote the rank of the hit(s), that match the annotated sequence(s). If the Rank column is empty, none of the annotated sequences was among the hits. The E-values are the range from the highest to the lowest rank.