RSmatch statistics

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RSmatch specifications

Information


Unique identifier OMICS_15916
Name RSmatch
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format FASTA
Operating system Unix/Linux
Computer skills Advanced
Version 1.2
Stability Stable
Maintained No

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Publication for RSmatch

RSmatch in pipeline

2007
PMCID: 1950533
PMID: 17586815
DOI: 10.1093/nar/gkm474

[…] c-box scoring matrix., rna structures were generated using the rnafold program from the vienna-rna-1.4 package (http://www.tbi.univie.ac.at/~ivo/rna/windoze/), structural alignment was done using rsmatch1.0 converted for windows (original program is available at http://exon.umdnj.edu/software/rsmatch/) and foldalignm (http://foldalign.ku.dk/software/index.html).rrna sequence alignments […]


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RSmatch in publications

 (6)
PMCID: 5657034
PMID: 29072145
DOI: 10.1186/s12859-017-1830-6

[…] $$\end{document}score percentageab=scoreabmaxabwhere max(a, b) = max {score(a, a), score(b, b.)}, rsmatch [], which is another alignment distance, is a tool for aligning rna secondary structures and is also used for motif detection. determined with widely used algorithms for rna folding, […]

PMCID: 4339682
PMID: 25727492
DOI: 10.1186/s12859-015-0464-9

[…] structures taken from rna starnd where the pseudoknot-free structures belonged to rfam [] (see additional file : table s3). we compared rkalign with three other tools: carna [], rnaforester [] and rsmatch []. rnaforester, included in the widely used vienna rna package [], is a versatile rna structure alignment tool. like rkalign and carna, an option of rnaforester is able to accept as input […]

PMCID: 3849165
PMID: 23722291
DOI: 10.4161/rna.25038

[…] software package called infernal (infernal.janelia.org)., a variety of other computational tools for rna homology search exist besides infernal.,,, some of the most popular tools are erpin, fastr, rsmatch, rnamotif, rnatops and patscan. infernal is one of the most generally applicable and powerful tools and is the basis for a widely used rna family database (rfam; described below). […]

PMCID: 3467077
PMID: 22821558
DOI: 10.1093/nar/gks684

[…] approach is often very computationally intensive., a number of programs have been applied to genome-wide identification of novel structured rnas (,), such as rnaz (), rna sampler (), evofold (), rsmatch (), foldalign (), cmfinder (), rnapromo () and locarna (). given the complexity and variety of structured rnas in a genome, the performance of different approaches differs considerably (,,). […]

PMCID: 2413145
PMID: 18439287
DOI: 10.1186/1471-2164-9-189

[…] to uncover conserved rna structures in utrs. we focused on small stem-loop structures. we compared folded rna structures in utr sequences for orthologous genes by our rna structure alignment tool rsmatch []. similar orthologous structures were then compared in an all-against-all fashion to derive rna structure groups. using cluster analysis and gene ontology (go) information, we identified […]


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RSmatch institution(s)
Department of Biochemistry and Molecular Biology, New Jersey Medical School, University of Medicine and Dentistry of New Jersey, Newark, NJ, USA; Department of Computer Science, New Jersey Institute of Technology, University Heights, Newark, NJ, USA

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