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The following table illustrates the results of similar full structures search. The query structures are structures extracted from the RFam randomly chosen and not being part of the alignments seeds. The search was carried out only on the alignements seeds structures of the RFam. A search is considered successful ("Success") if at least 3 of the 5 best matching structures and the query structure share the same family; it is unsuccessful ("Not found") if the score of the best corresponding structure is bad (negative or close to 0); finally, a search is a failure ("Failed") if at least 3 of the 5 best found corresponding structures are from different families that the one of the query structure and despite everything, the scores remain good (above 0).


#Query Structure NameQuery Structure FamilyBest MatchesResult
Structure NameFamilyScore
 
1 BA000007.2/232087-232202 5S_rRNA (5S ribosomal RNA) RS000325| AB035926.1/5989-6104| Escherichia coli O157:H7
RS000328| AF170176.1/1092-1207| Salmonella typhimurium LT2
RS000326| X02264.1/3-118| Plesiomonas shigelloides
RS000327| X02039.1/3-118| Proteus vulgaris
RS000316| X02250.1/3-118| Shewanella putrefaciens
5S_rRNA
5S_rRNA
5S_rRNA
5S_rRNA
5S_rRNA
169
165
164
161
159
Success
2 AB096745.1/13-160 5_8S_rRNA (5.8S ribosomal RNA) RS000608| U21939.1/68-218| Plasmodium falciparum (malaria parasite P. falciparum)
RS000642| X53538.1/2090-2241| Herdmania momus
RS000634| X90410.1/15-165| Blastocladiella emersonii
RS000612| AF223571.1/210-358| Euplotes aediculatus
RS000639| L78065.1/3758-3910| Anopheles albimanus
5_8S_rRNA
5_8S_rRNA
5_8S_rRNA
5_8S_rRNA
5_8S_rRNA
87
82
78
76
71
Success
3 AF162900.1/1-125 5_8S_rRNA (5.8S ribosomal RNA) RS000637| M21017.1/2722-2844| Drosophila melanogaster (fruit fly)
RS013731| J04118.1/2-131| Homo sapiens (human)
RS002342| X58844.1/2-130| Tetrahymena thermophila
RS003329| AF311938.1/7320-7445| Human echovirus 30
RS006749| L12224.1/171-292| Pseudomonas syringae
5_8S_rRNA
U11
U4
Entero_OriR
RsmY
-26
-133
-∞
-∞
-∞
Not found
4 AP004064.3/91158-91354 U2 (U2 spliceosomal RNA) RS000815| AF106847.1/185-380| Oryza sativa
RS000817| AF106845.1/1870-2065| Oryza sativa
RS000820| X69327.1/1-196| Triticum aestivum (bread wheat)
RS000816| AF106845.1/257-451| Oryza sativa
RS000819| S72337.1/1-193| Triticum aestivum (bread wheat)
U2
U2
U2
U2
U2
300
288
287
285
274
Success
5 D14894.1/1-82 tRNA RS001193| K00228.1/1-82| Saccharomyces cerevisiae (baker's yeast)
RS001855| AC122544.1/63069-62986| Solanum lycopersicum
RS001874| M21542.1/51-134| Phaseolus vulgaris
RS001208| X56506.1/61-144| Saccharomyces cerevisiae (baker's yeast)
RS001503| Z54587.1/126-45| Homo sapiens (human)
tRNA
tRNA
tRNA
tRNA
tRNA
105
105
103
99
97
Success
6 AC068228.8/108119-107905 U3 (Small nucleolar RNA U3) RS014182| AF176810.1/1-214| Bos taurus (cattle)
RS014178| M23705.1/702-916| Mus musculus (house mouse)
RS014180| J01884.1/1-215| Rattus norvegicus (Norway rat)
RS014181| X14945.1/538-754| Homo sapiens (human)
RS014179| X63743.1/815-1027| Mus musculus (house mouse)
U3
U3
U3
U3
U3
194
191
189
183
173
Success
7 AY009860.1/9-218 Intron_gpI (Group I catalytic intron) RS002843| M22563.1/302-518| Cyanophora paradoxa
RS002748| U45437.1/191-400| Paramecium caudatum
RS002749| U45434.1/113-327| Paramecium primaurelia
RS003368| D00591.1/3109-3311| Homo sapiens (human)
RS003369| AL513497.21/8055-8258| Homo sapiens (human)
Intron_gpI
Telomerase-cil
Telomerase-cil
SNORA73
SNORA73
-62
-134
-139
-139
-141
Not found
8 AF312965.1/449-3 Intron_gpI (Group I catalytic intron) RS002852| M16898.1/110-597| Nicotiana tabacum (common tobacco)
RS002851| X86563.2/48991-49433| Zea mays
RS002853| M55084.1/84-519| Vicia faba (fava bean)
RS002848| X15850.1/1348-1752| Chlamydomonas moewusii
RS002092| AF186224.1/13-452| Saccharomyces dairenensis
Intron_gpI
Intron_gpI
Intron_gpI
Intron_gpI
RNaseP_nuc
282
111
64
-420
-∞
Success
9 AY497285.1/1484-1542 Intron_gpII (Group II catalytic intron) RS002890| X04465.1/754-816| Marchantia polymorpha (liverwort)
RS002949| X17395.1/1934-1994| Petunia x hybrida
RS002898| X04465.1/77203-77142| Marchantia polymorpha (liverwort)
RS002917| X01088.1/1893-1955| Oryza sativa
RS002932| X63625.1/1815-1875| Daucus carota (carrot)
Intron_gpII
Intron_gpII
Intron_gpII
Intron_gpII
Intron_gpII
54
48
46
43
43
Success
10 AY944142.1/1474-1813 RRE (HIV Rev response element) RS003145| AF217173.1/1552-1888| Human immunodeficiency virus 1
RS003163| AF112547.1/1447-1786| Human immunodeficiency virus 1
RS003185| AF003887.1/7736-8075| Human immunodeficiency virus 1
RS003146| AF025754.1/1489-1825| Human immunodeficiency virus 1
RS003176| U79722.1/1497-1833| Human immunodeficiency virus 1
RRE
RRE
RRE
RRE
RRE
583
581
580
580
578
Success
11 AB124885.1/2114-2034 SNORD36 (Small nucleolar RNA SNORD36) RS003466| AB052962.1/8100-8020| Oryza sativa
RS003468| AB052962.1/7854-7779| Oryza sativa
RS005466| AJ490395.1/1-83| Oryza sativa
RS003469| AB052962.1/8576-8491| Oryza sativa
RS005465| AJ490400.1/1-82| Oryza sativa
SNORD36
SNORD36
snoZ168
SNORD36
snoZ168
93
66
65
65
63
Success
12 M74805.1/4-226 IRES_HCV (Hepatitis C virus internal ribosome entry site) RS004414| L27875.1/1-232| Hepatitis C virus
RS003821| L27901.1/1-232| Hepatitis C virus
RS003928| L27902.1/1-231| Hepatitis C virus
RS004038| L27903.1/1-231| Hepatitis C virus
RS004608| L27898.1/1-231| Hepatitis C virus
IRES_HCV
IRES_HCV
IRES_HCV
IRES_HCV
IRES_HCV
389
387
385
385
385
Success
13 AF245283.1/1-183 IRES_HCV (Hepatitis C virus internal ribosome entry site) RS004019| AF134751.1/1-181| Hepatitis C virus
RS004239| AF463477.1/1-178| Hepatitis C virus
RS004268| AF463491.1/1-178| Hepatitis C virus
RS004332| AY190455.1/1-181| Hepatitis C virus
RS004455| D13450.1/1-184| Hepatitis C virus
IRES_HCV
IRES_HCV
IRES_HCV
IRES_HCV
IRES_HCV
172
172
171
159
146
Success
14 AE017279.1/213993-213872 SAM (SAM riboswitch (S box leader)) RS005484| Z99109.2/169069-168952| Bacillus subtilis subsp. subtilis str. 168
RS005503| AL591974.1/109385-109266| Listeria monocytogenes
RS005502| AL596164.1/95936-95817| Listeria innocua
RS005486| Z99110.2/47875-47995| Bacillus subtilis subsp. subtilis str. 168
RS005497| AL591983.1/96176-96058| Listeria monocytogenes
SAM
SAM
SAM
SAM
SAM
106
99
97
96
80
Success
15 AF311956.1/10643-10735 Flavi_CRE (Flavivirus 3' UTR cis-acting replication element (CRE)) RS006624| AF226686.1/10643-10735| Dengue virus type 1
RS006622| AY099346.1/2415-2507| Dengue virus type 3
RS006623| AF204178.1/10631-10723| Dengue virus type 2
RS006609| AF022438.1/10631-10723| Dengue virus type 2
RS006628| AF169684.1/10631-10723| Dengue virus type 2
Flavi_CRE
Flavi_CRE
Flavi_CRE
Flavi_CRE
Flavi_CRE
162
161
160
159
159
Success
16 AJ295189.1/350-601 IRES_Picorna (Picornavirus internal ribosome entry site (IRES)) RS007300| AY278550.1/389-640| Human poliovirus 2
RS007283| AY278551.1/389-640| Human poliovirus 2
RS007271| AJ288062.2/207-458| Human poliovirus 2
RS007246| AF499642.1/390-641| Human coxsackievirus A20
RS007285| AF448782.1/393-644| Human poliovirus 2
IRES_Picorna
IRES_Picorna
IRES_Picorna
IRES_Picorna
IRES_Picorna
413
411
397
389
385
Success
17 AF542425.1/186-354 IRES_Picorna (Picornavirus internal ribosome entry site (IRES)) RS010696| AL035300.1/11215-11044| Mycobacterium leprae
RS010701| Z99110.2/185182-185347| Bacillus subtilis subsp. subtilis str. 168
RS010697| AE017239.1/279457-279627| Mycobacterium avium subsp. paratuberculosis K-10
RS010715| AE016950.1/98937-98770| Enterococcus faecalis V583
RS010712| AE016957.1/74880-75046| Enterococcus faecalis V583
ykoK
ykoK
ykoK
ykoK
ykoK
-196
-197
-200
-202
-206
Not found
18 AL591206.9/7281-7151 SCARNA8 (Small Cajal body specific RNA 8) RS008393| AY077742.1/1-131| Homo sapiens (human)
RS008392| AL824707.7/136518-136388| Mus musculus (house mouse)
RS004883| U64704.1/88-217| Oryctolagus cuniculus (rabbit)
RS004882| U64707.1/102-229| Gallus gallus (chicken)
RS014085| AC007025.2/13587-13714| Homo sapiens (human)
SCARNA8
SCARNA8
SNORA63
SNORA63
SNORA35
209
152
50
49
48
Failed
19 AF317944.1/3-91 snosnR60_Z15 (Small nucleolar RNA snR60/Z15/Z230/Z193/J17) RS008499| AF317944.1/1-91| Arabidopsis thaliana (thale cress)
RS004691| AJ240063.1/2-93| Arabidopsis thaliana (thale cress)
RS008690| AF317938.1/3-92| Arabidopsis thaliana (thale cress)
RS011862| AE016815.2/457650-457564| Eremothecium
RS011841| CR380957.1/1049740-1049827| Candida glabrata CBS 138
snosnR60_Z15
SNORD24
snoR11
snosnR61
snosnR54
113
71
70
67
67
Failed
20 AY965481.1/297-380 HIV_GSL3 (HIV gag stem loop 3 (GSL3)) RS010535| AF116065.1/50-133| Human immunodeficiency virus 1
RS010311| Z97087.1/19-102| Human immunodeficiency virus 1
RS009325| AF386032.1/65-148| Human immunodeficiency virus 1
RS009289| AF017841.1/14-97| Human immunodeficiency virus 1
RS010197| AB042488.1/65-148| Human immunodeficiency virus 1
HIV_GSL3
HIV_GSL3
HIV_GSL3
HIV_GSL3
HIV_GSL3
101
85
85
85
85
Success
21 BX324133.12/13562-13615 UnaL2 (UnaL2 LINE 3' element) RS008336| AF357378.1/1-59| Mus musculus (house mouse)
RS014568| AF357318.1/1-59| Mus musculus (house mouse)
RS008677| AF357332.1/1-59| Mus musculus (house mouse)
RS004936| AE010246.1/8197-8144| Pyrococcus furiosus DSM 3638
RS004948| AF254829.1/1-52| Pyrococcus abyssi
SNORD57
SNORD110
snoZ50
snoPyro_CD
snoPyro_CD
130
130
130
124
121.5
Failed
22 AY779563.1/1371-1422 HIV_FE (HIV Ribosomal frameshift signal) RS012456| AY255816.1/1280-1331| Human immunodeficiency virus 1
RS012353| AY140137.1/1034-1085| Human immunodeficiency virus 1
RS012212| AJ006022.1/1658-1709| Human immunodeficiency virus 1
RS012474| M73472.1/3-54| Human immunodeficiency virus 1
RS012159| AF457057.1/1284-1335| Human immunodeficiency virus 1
HIV_FE
HIV_FE
HIV_FE
HIV_FE
HIV_FE
109
107
105
105
104.5
Success
23 AF165060.1/354-506 HCV_ARF_SL (Hepatitis C alternative reading frame stem-loop) RS013715| AE003539.3/169065-169217| Drosophila melanogaster (fruit fly)
RS013714| AE003539.3/168888-169040| Drosophila melanogaster (fruit fly)
RS014992| D38078.1/363-515| Hepatitis C virus
RS014871| D37845.1/363-515| Hepatitis C virus
RS014678| D37846.1/363-515| Hepatitis C virus
snopsi28S-3327
snopsi28S-3327
HCV_ARF_SL
HCV_ARF_SL
HCV_ARF_SL
277
275
274
274
274
Success
24 D38629.1/558-610 IRES_APC (APC internal ribosome entry site (IRES)) RS004936| AE010246.1/8197-8144| Pyrococcus furiosus DSM 3638
RS004924| AF254824.1/1-52| Pyrococcus abyssi
RS004948| AF254829.1/1-52| Pyrococcus abyssi
RS004940| AF254836.1/1-50| Pyrococcus abyssi
RS008575| AF357327.1/1-48| Mus musculus (house mouse)
snoPyro_CD
snoPyro_CD
snoPyro_CD
snoPyro_CD
snoMBII-202
122
119.5
119.5
117
114.5
Failed
25 AJ784367.2/1-75 snoMe18S-Gm1358 (Small nucleolar RNA Me18S-Gm1358) RS011869| AJ617330.1/1-80| Schizosaccharomyces pombe (fission yeast)
RS011836| AE016818.1/862034-862113| Eremothecium
RS008496| AY220644.1/1-79| Oryza sativa
RS011860| AJ575660.1/49220-49297| Yarrowia lipolytica
RS011873| AF085227.1/271-347| Mayetiola destructor (Hessian fly)
snosnR61
snosnR54
snosnR60_Z15
snosnR61
snosnR61
191.5
191.5
190
189
187.5
Failed
Table I: Full structures search results. (nb. used structures are inside comments in HTML source code)