Fisher: a program for the detection of H/ACA snoRNAs using MFE secondary structure prediction and comparative genomics – assessment and update

Table 1 S. cerevisiae candidate snoRNAs found by Fisher for rRNA pseudouridylation sites.

Candidate	Detected on N Blot	ψ-map^a	ψ-site	Chromosome	Position^b	Homologues detected in other yeast genomes^{c, d}													snoRNA^e
						Sp	Sm	Sk	Se	Sb	Cg	Sc	Kl	Sl	Kw	Ag	Dh	Ca
1	N	7	SSU₇₅₉	XV	87507>87772	+				+
2	Y	7	SSU₇₅₉	V	52135<52357	+	+	+		+	+	+	+		+	+		+	snR80
3	NP	13	SSU₁₂₉₀	IV	562489>562750	+		+
4	N	14	SSU₁₄₁₅	XIII	302531>302787	+	+
5	N	14	SSU₁₄₁₅	XIII	556582>556828	+	+	+										+
6	NP	15	LSU₇₇₆	II	483358>483595	+	+	+	+
7	Y	15	LSU₇₇₆	V	52135<52357	+	+	+		+	+	+	+		+	+		+	snR80
8	NP	22	LSU₁₀₅₂	V	517714>517935	+	+	+
9	NP	22	LSU₁₀₅₂	XV	234298>234538		+	+		+									snR81
10	N	33	LSU₂₃₁₄	XIV	91706<91951	+	+	+
11	Y	33	LSU₂₃₁₄	XIII	762101<762294	+	+	+		+					+	+			snR86
12	NP	35	LSU₂₃₄₉	VII	316840>317063	+	+	+		+	+	+		+					snR82
13	NP	35	LSU₂₃₄₉	X	519129>519328	+	+	+		+
14	NP	35	LSU₂₃₄₉	VIII	271983>272251	+		+

^acorresponds to ψ-map numbering as given in Table S1, Additional file 2.
^b'>' indicates the candidate is on the Watson strand, and '<' indicates it is on the Crick strand in S. cerevisiae.
^cAbbreviations: Sp – S. paradoxus; Sm – S. mikatae; Sk – S. kudriavzevii; Se – S. exiguus; Sb – S. bayanus; Cg – C. glabrata; Sc – S. castellii; Kl – K. lactis; Sl – S. kluyveri; Kw – K. waltii; Ag – A. gossypii; Dh – D. hansenii; Ca – C. albicans.
^dN.B. no homologues were detected in Y. lipolytica or S. pombe, though both were screened; S. exiguus partial genome sequence from Génolevures [28].
^eSnoRNAs identified by snoGPS [3] or experimentally [2] which we were also able to identify using Fisher.
^fY: detected; N: not detected; NP: Not performed.

ISSN: 1756-0500