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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 Name | Query Structure Family | Best Matches | Result | ||
|---|---|---|---|---|---|---|
| Structure Name | Family | Score | ||||
| 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 |

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