LocARNA specifications

Information


Unique identifier OMICS_03736
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


  • SPARSE
  • ExpaRNA-P
  • LocARNA-P

Documentation


Maintainer


  • person_outline Rolf Backofen <>

Information


Unique identifier OMICS_03736
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


  • SPARSE
  • ExpaRNA-P
  • LocARNA-P

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Rolf Backofen <>

LocARNA articles

LocARNA citation

2017
PMCID: 5737618

[…] 2–8 of the mature mirna; see supplementary table 4, supplementary material online). for the conserved mirna seed families, seed-constrained multiple sequence alignments were constructed using locarna (will et al. 2007, 2012), which takes the predicted secondary structure of the mirnas into account. for each mirna group, the similarity matrix (locarna scores) was transformed […]

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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