ExpaRNA - Exact Matching

ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs. A motif is a local (or isolated) substructure which is identical to both RNAs. ExpaRNA requires a given nested secondary structure for both RNAs. If no structure is available, RNAfold from Vienna RNA Package is used for a structure prediction. The accuracy of the algorithm is mainly controlled by the minimal size of the included sequence-structure motifs. ExpaRNA is especially useful for comparative structural RNA analysis and to speed-up complex sequence-structure alignment methods. For this purpose, the predicted common substructures by ExpaRNA are used as anchor constraints for a full structural alignment.

For articles describing the tool and webserver refer to the reference section below. Please cite us when using our tools.
For more information check the help page.

Try ExpaRNA with these examples:

large (input|result)
small (input|result)

Input Parameter

Sequence Input in FASTA Format:

[clear]

>J01695_Ecoli_16SrRNA
AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
........(((((.......))))).((((.((((((.(((((((((....(((.(((..(((..(((((..((((((((((....))))))).))))).))))))......(((......((((((((.((...(((((((.((((....(((((((....))))))).....)))).....(((....)))....((((((..((....)))))))).)))))))..))))))))))(((..(.(((..((((((((.......))))))))))).....))))..((((((((....))))...))))))).((((((..........)))))).((((....))))...)))))).).....(.(((...(((((....))))).)))).)).))))))..((((......((((....)))).....))))....((((((...(....((((((((.......)))))))).....)....))))))......(((((......(((((.....((....)).......)))))))))).))))))))))..........(((.....(.((((.(.(((.(((((((.(((((((((((....(((((((.....)))))))..)))))))))..)))))))))...(((((((((..(((((((((..((((((((...(((......)))......))))))))..))....(..((....)))))))))).))))).))))...))))..))))....((((((...((...((((.........))))...))))))))..........((((((..((((((((((((.....))))))))))))...((....)).....)))))))))).(((......((((....))))....)))........(((((.(((((((.((..(((((((((((((((((....((((........))))........(((((((.....((((((((..(((((((....))))))).((((....))))))))).))).((.((((..(((((((((...(((((((((....)))..((((......))))..)))))).....((((.(((((((...((..(((.....)))))....)))))))..((((((((.....)))))))).....))))....)))).)))...))))))))....)))))))...)).))))))))))...(((((((.....(((..((...(((....)))...))....))).....)))))))......(...((((((((........))))))))...).....))))).....((((((((.......))))))))......))...)))))))))).))..(.((.((.(.((((((((..((((((((((((....((((((.((((..((....)).))))))))))...))))))))))))..))))))))..).))..))..).((((((((((....))))))))))............. #FS
>Ddiscoideum_16SrRNA
AAGAAAAAAAUGAGUUUGAUUCUGGCUCCGAAUGAAUGCUAUCAGUGGGCUUUAUACAUGCAAGUUGAACGCUAUUGAAAAAUAGAGUAGCAAAAAGGUGAGUAAUGCAUAUGAAUUUUAAUAAUAAUUUUGGGAAUAAAAGAAGAAAUCCAGAAUAAAAAGAAAGAGGAACUUGAAAAACAGUAAGACUCGUUAUUAUAAAAGCGUAUGUCGAAUUAGGCAGUUGGUGGGGUAAAGGCUUACCAAACCUGAGAUUCGUAGGUGGUUCGAGAGAAUGAUCAUCCACAUUGGUAUUGAAAGAACGACCAAACUCUGAAGAGGCUGCAGUAAGGAAUAUUGGACAAUGAGCGCAAGCUUGAUCCAGCUACACUGAGUGAGGGAAGAAGUAAAGCGUAAACCUCUUUUAAUAAGGAAGAUAAUGACAAAAAUUAAAGAAGAAGUCCCGGCUAAUUUCGUGCCAGCCGCCGCGGUAAUACGGAGGGGGCAAGCAUUAUUCGUAAGGAUUGGGCGUAAAGGGUGCGUAGGCUGGUUCUCAAAGGUAUUAUAUGAAAAACACUGAAAAAAGAGGUGUGGGUAUAAAAACAAACAAAGAACCUAGAGUAAAGAUGAUGUAUUUAGAAGAACUAAUCUAGAGGUAAAAUUCAAUUUAGAUUAGUUUGACUGACAGUUGGCGAAGGCAAAAUACAAGCAAUACUGACGCUAAAGCACGAAGGUUCAGGGAGCAAAUCGGAUUAGAGACCCGAGUAGUCUGAACAGUAAACGAUGAGUGUUCAAUAUUCUAAAAAGUAUUUGAGUUAACACGUUAAACACUCCGCCUGAGUAGUACGAUCGCAAGAUUGAAACUCAAGGUAAUUGACGGAACUUUGCGCAAGCAGUGGAUUAUGUUCAUUAAUUUGAUACAACACGAAAAAUCUUACCCUCCAUUGAAUGACAUAUAUAAAACAUGAAACAAAUGUGAAGAAUAGAAGCAGACAAGGUUCUAUUAAAAUAAAUGUCUAACAGGUGUUGCAUGGCUGUCGUCAGUUCGUGCUGUGAGGUGUAACAUUAAGUUGUGAAACGAACGAAAUCCUUAAGUUCAAUUACGAUAUAUAAUCGAGAAAUGGACAGAAGAGUGUGACAUAAAUUAAAUCACAUUGGUAGUUGAGGAAGAUGUCAAGUCAGUAUGGCCCUUAUAGGAGGGGCUUGAAAUGUAAUACAAUGGUUUCUACAAAAGGAAGCGAAAGUGCAAGCUGGAGCAAAACCUAAAAAGAAAUCUUAGUUUGGAUUUAUUUCUGCAACUCGAAAUAAUGAAAGCGGAAUUGCUAGUAAUCGUAGAUCAUAAGGCUUCGGUGAAUAGUUGUCAAAGUUAGUACAUACCGCCCGUCACACCACGGAAAUCAAUCUUUUUCAGAUACAUUAUUAUGUUAAUUAUCUAAAGUUCUUAGGGUAUAACAGUCUCUUUUGAAGAGCAAUUAGAAUGGAGGAGGUUAAUUGUUAAUUAUCGAACAAUAGAGGGGUAACUGGGGUAAAGUCGUAACACGGUAGCUGUUGGGGAACCAGUAGCUGGAAGUA
...........(((((.......))))).((((.((((((.((((((((.....(((.(((..(((..((((((((....)))))))))))......(((......(((((((..((...(((((((.((((((..............))))))......................................)))))))..)).)))))))(((..(.(((..((((((((.......))))))))))).....))))..((((((((....))))...))))))).(((((((........))))))).(((....)))...)))))).......(.(((...(((((....))))).)))).)).))))))..((((......((...)).....)))).(....((((...(.......)....))))....)...(((((......(((((.....((....)).......)))))))))).))))))))))..........(((.......((((...(((((((((((..(((((((((((.....(((((.........)))))..)))))))))))...)))).)))...((((((((...(((((((((((((((((((...(((......))).......)))))))))))).....(..((....)))))))))).))))))))..))))...))))....(((((((...(...((((.........))))...))))))))..........(((((((...((((......)))).....((....))....))))))).))).(((......((((....))))....)))........(((((.(((((((....((((((.(((((((((((....((((........))))........(((((((.....((((((.........................................................))))))...(((.(((..(((((((((((..(((((((((....)))...(((......)))...)))))).....(((((.(((((....((((.....)))).....))))).....(((((((...........)))))))......)))))...))))).)))...)))))))))...)))))))...)).)))))))))....(((((((.....(((..((...(((....)))...))....)))....)))))))......(...((((((((........))))))))...).....))))))....((((((((.......))))))))..........)))))))))).))....((.((.(.((((((((..............................................................................................................................))))))))..).))..))....((((((((((....))))))))))...... #FS

Minimal size of included substructures:

Maximal number of used substructures:
(0 = all)

EPM scoring:

just EPM size (default)
EPM^2 = prefer larger patterns

Output Parameter

Write ExpaRNA result as input for LocARNA with anchor constraints:

Write ExpaRNA result as alignment into text file:

Write ExpaRNA results as list in file:

Write all EPMs into file:

Description:

Your Email:

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When using ExpaRNA please cite :

Steffen Heyne, Sebastian Will, Michael Beckstette, and Rolf Backofen
Lightweight comparison of RNAs based on exact sequence-structure matches
Bioinformatics, 25 no. 16 pp. 2095-2102, 2009
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with ExpaRNA version 1.0.0 linking Vienna RNA package 1.8.5

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ExpaRNA - Exact Matching

Input Parameter

Output Parameter

When using ExpaRNA please cite :