LocARNA statistics

info info

Citations per year

Number of citations per year for the bioinformatics software tool LocARNA
info

Tool usage distribution map

This map represents all the scientific publications referring to LocARNA per scientific context
info info

Associated diseases

This word cloud represents LocARNA usage per disease context
info

Popular tool citations

chevron_left Multiple nucleotide sequence alignment Folding prediction Sequence-structure pattern search chevron_right
Want to access the full stats & trends on this tool?

Protocols

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


download.png
github.png
conda.png

Versioning


No version available

Documentation


Maintainer


  • person_outline Rolf Backofen

Publications for LocARNA

LocARNA citations

 (81)
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

[…] penSUSE 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) (). […]

call_split

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
call_split See protocol

[…] of species and associated identification numbers used in this study is given as Supplementary Table .A combined multiple sequence-structure alignment of the data set sequences were obtained applying LocARNA version 1.8.1 with the option local-progressive followed by RNAalifold from the ViennaRNA package version 2.1.8-2. […]

library_books

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

2018
Front Genet
PMCID: 5780412
PMID: 29403526
DOI: 10.3389/fgene.2017.00231

[…] LocARNA is a tool for RNA sequence multiple alignments (Will et al., , ; Smith et al., ). The LocARNA multiple alignments are shown in conjunction with the predicted structure by RNAalifold (Bernhart […]

library_books

Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs

2018
Front Microbiol
PMCID: 5758548
PMID: 29354101
DOI: 10.3389/fmicb.2017.02582

[…] erfaces in early 2000s (Zuker, ).In contrast to folding one sequence at a time [single-sequence methods e.g., mfold/UNAfold (Zuker, ), RNAfold (Gruber et al., )], a new generation of software such as LoCARNA (Smith et al., ) and RNAz (Gruber et al., ) work on multiple sequences (comparative methods). This alleviates the need of predicting RNA structures from related virus sequences one at a time a […]

call_split

DotAligner: identification and clustering of RNA structure motifs

2017
Genome Biol
PMCID: 5747123
PMID: 29284541
DOI: 10.1186/s13059-017-1371-3
call_split See protocol

[…] score saturates after 1000 samples of the stochastic backtracking for T=0.25 (Additional file : Figure S2B). CARNA version 1.2.5 was run with parameters --write-structure --noLP --time-limit=120000. LocaRNA version 1.7.13 was run with parameter --noLP. FoldAlign version 2.1.1 was run with and without parameter -global. Default parameters were used for pmcomp, downloaded from https://www.tbi.univi […]

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

[…] nd 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 of all window […]


Want to access the full list of citations?
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.’’

LocARNA reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review LocARNA