LocARNA protocols

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LocARNA specifications

Information


Unique identifier OMICS_03736
Name LocARNA
Software type Package/Module
Interface Command line interface, Web user interface
Restrictions to use None
Input data Set of RNA sequences
Input format FASTA
Output data Multiple alignment of the input sequences
Programming languages C++
License GNU General Public License version 3.0
Computer skills Basic
Version 1.8.12
Stability Stable
Maintained Yes

Subtools


  • ExpaRNA-P
  • LocARNA-P
  • SPARSE

Documentation


Maintainer


  • person_outline Rolf Backofen <>

Information


Unique identifier OMICS_03736
Name LocARNA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Set of RNA sequences
Input format FASTA
Output data Multiple alignment of the input sequences
Operating system Unix/Linux, Mac OS
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.8.12
Stability Stable
Maintained Yes

Subtools


  • ExpaRNA-P
  • LocARNA-P
  • SPARSE

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Rolf Backofen <>

Publications for LocARNA

LocARNA in pipelines

 (13)
2017
PMCID: 5737618
PMID: 29036592
DOI: 10.1093/gbe/evx197

[…] the identity of their seed sequences (positions 2–8 of the mature mirna; see , online). for the conserved mirna seed families, seed-constrained multiple sequence alignments were constructed using locarna (, ), which takes the predicted secondary structure of the mirnas into account. for each mirna group, the similarity matrix (locarna scores) was transformed into a distance matrix […]

2014
PMCID: 4041456
PMID: 24753415
DOI: 10.1093/nar/gku283

[…] needleman–wunsch + mbr with those obtained using other six alignment methods, namely a sequence-only version of the needleman–wunsch, as implemented in the ‘needle’ tool from the emboss package (), locarna (), rnastrat (), rnadistance and rnaforester (both included in vienna package) and gardenia ()., we used the sum-of-pairs score (sps) () as a measure to evaluate the performances […]

2014
PMCID: 4053861
PMID: 24393626
DOI: 10.1186/gb-2014-15-1-r7

[…] either unafold or the viena rna package with default parameter settings [,]. secondary structures of the predicted rnas were drawn using varna []. structure alignment of ncrnas was performed using locarna (global standard alignment) []. single stranded regions of the known snrnas were used to screen for mrna sequence complementarity with these regions using rnahybrid []. the minimum free […]

2014
PMCID: 4164361
PMID: 25222120
DOI: 10.1371/journal.pone.0106545

[…] with 99% sequence identity and 99% coverage . sequences of representatives of non-redundant sets are provided in fasta format (). all representatives in the non-redundant datasets were aligned using locarna software using default parameters . locarna first calculates the secondary structure for all isr using rnafold and then generates a multiple alignment that conserves as many structural […]

2014
PMCID: 4254888
PMID: 25512885
DOI: 10.1186/2193-1801-3-684

[…] (http://its2.bioapps.biozentrum.uni-wuerzburg.de/) (koetschan et al. ; merget et al. ; koetschan et al. ) was used. consensus secondary structures for the its1 and 5.8s markers were determined using locarna-p simultaneous rna alignment and folding option of the freiburg rna tools pipeline (http://rna.informatik.uni-freiburg.de:8080/locarna/input.jsp) (will et al. , will et al. and smith et al. […]


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LocARNA in publications

 (83)
PMCID: 5913331
PMID: 29719549
DOI: 10.3389/fgene.2018.00124

[…] 42.2 leap and installed rnalien version 1.3.7. furthermore, we installed the following dependencies: rnaz (v2.1) (), viennarna package (v2.3.4) (), infernal (v1.1.2) (), rnacode (v0.3) () and locarna (v1.9.2) ()., for the synteny analysis, amino acid sequences of all protein-coding genes overlapping a window 3 kb up- and downstream of the srna locus were extracted from the respective […]

PMCID: 5857606
PMID: 29593672
DOI: 10.3389/fmicb.2018.00395

[…] complement of the plus strand 5′ utr but not further upstream in the minus strand. our predictions (data not shown) of the conserved structure upstream of the sl iv′ in the minus strand using the locarna program () reveal that the reverse complement sequence of the sl v in the minus strand does not form a conserved mirror of the sl v structure in the plus strand, whereas the sl vi′ and 588′ […]

PMCID: 5775257
PMID: 29352114
DOI: 10.1038/s41467-017-02582-1

[…] structures in vitro. additionally, crosslinking and immunoprecipitation experiments showed interaction with predicted u-rich stem-loops of different lengths in cells. therefore, we employed the locarna algorithm for the identification of evolutionary conserved structured motifs within the mapped region of the icos 3′-utr. two conserved stem-loops, an octa-loop with a u-rich loop […]

PMCID: 5730773
PMID: 29046452
DOI: 10.1128/JVI.01159-17

[…] unpaired sequence at the top of the predicted stem loops (). the sequences spanning these predicted structures were compared with the equivalent sequences in 59 diverse type o virus isolates using locarna () to identify conservation of predicted rna structures. this showed that despite variation in primary sequence between isolates, there was conservation of the base pairing required […]

PMCID: 5770649
PMID: 29375488
DOI: 10.3389/fmicb.2017.02432

[…] experimental confirmation and also validated the utr bioinformatics prediction methods., given that structural conservation is closely associated with the regulatory roles of rna (yang et al., ), locarna was used to determine conservation based on both sequence and structure (will et al., ). ncbi blast (camacho et al., ) was used to identify sequence homology for each 5′utr candidate, […]


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LocARNA institution(s)
Chair for Bioinformatics, Institute of Computer Science, Albert-Ludwigs-Universität, Freiburg, Germany; CSAIL and Mathematics Department, Computation and Biology Group, MIT, Cambridge, MA, USA; Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Kongens Lyngby, Denmark; Department of Theoretical Chemistry, University of Vienna, Vienna, Austria; Bioinformatics Group, Department of Computer Science, Interdisciplinary Center of Bioinformatics, University of Leipzig, Leipzig, Germany; Max-Planck-Institute for Mathematics in the Sciences, Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany; Santa Fe Institute, Santa Fe, NM, USA; Center for Biological Signaling Studies (BIOSS), University of Freiburg, Freiburg, Germany;
LocARNA funding source(s)
This work was supported by the German Research Foundation (grants BA 2168/3-1 as well as BA 2168/2-2, STA 850/7-1 [under the auspices of SPP-1258 ‘‘Sensory and Regulatory RNAs in Prokaryotes’’], the Excellence Initiative of the German Federal and State Governments [EXC 294], and WI 3628/1-1); ESF grant no. 14494 (administered by the Sächsische AufbauBank); the German Federal Ministry of Education and Research (BMBF grant 0313921 FRISYS); and the Austrian Gen-AU project ‘‘Regulatory ncRNAs.’’

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