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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


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Versioning


No version available

Documentation


Maintainer


  • person_outline Rolf Backofen

Publications for LocARNA

LocARNA citations

 (86)
library_books

GLASSgo – Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence

2018
Front Genet
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 […]

library_books

Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication

2018
Front Microbiol
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′ […]

library_books

Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA

2018
Nat Commun
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 […]

library_books

Deep Sequencing of Foot and Mouth Disease Virus Reveals RNA Sequences Involved in Genome Packaging

2017
J Virol
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 […]

library_books

Identification and Characterization of 5′ Untranslated Regions (5′UTRs) in Zymomonas mobilis as Regulatory Biological Parts

2017
Front Microbiol
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, […]

library_books

Alignment free comparative genomic screen for structured RNAs using coarse grained secondary structure dot plots

2017
BMC Genomics
PMCID: 5712110
PMID: 29197323
DOI: 10.1186/s12864-017-4309-y

[…] memory usage for any practical use. to circumvent this problem, restricted, approximated or alternative versions of the sankoff-style algorithm, including foldalign [–], dynalign [–], cmfinder [], locarna [, ], murlet [], raf [] and dafs [], have been published with/without application to ncrna discovery. however, these methods are still too slow to perform an all-against-all scan […]


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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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