RNAz protocols

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RNAz specifications

Information


Unique identifier OMICS_17766
Name RNAz
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, Perl
Computer skills Advanced
Version 2.1
Stability Stable
Maintained Yes

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Additional information


http://www.tbi.univie.ac.at/~wash/RNAz/#documentation

Publications for RNAz

RNAz in pipelines

 (8)
2013
PMCID: 3783177
PMID: 23847102
DOI: 10.1093/nar/gkt596

[…] the alignments are then scored with sissiz version 2.0 () (updated binaries can be downloaded from the supplementary information) using default parameters (‘-j’ option for ribosum scoring) and with rnaz version 2.0 () using the following parameters: ‘-f -d’ for mafft alignments; ‘-f -t -l’ for native rfam structural alignments. finally, the subalignments are saved and the process is reiterated […]

2011
PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] rna structure searches is they have high false positive rates, around 50% . furthermore, a comparison of the encode regions that comprise one percent of the human genome show little overlap between rnaz, evofold, and cmfinder. even though the methods work in quite different ways, they all aim to fulfill the same task. this clearly shows that the area still needs to mature. a future direction […]

2011
PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] has been initiated in this area ., compensating base pairs are clearly important, even though systematic analyses to study the impact have not been carried out. as discussed in , the overlap between rnaz, evofold, and cmfinder on the encode regions was poor, and a main difference was that a substantial amount of cmfinder candidates had more and more of the maf blocks re-aligned as sequence […]

2009
PMCID: 2659441
PMID: 19343219
DOI: 10.1371/journal.pcbi.1000338

[…] in the sequence window only if at least two of all the pairwise alignments were predicted to contain an rna motif by qrna., we thank stefan washietl for insightful discussion on the svm model in rnaz. we also thank zizhen yao and andrew uzilov for discussions about using cmfinder and dynalign+libsvm., the authors have declared that no competing interests exist., this work was supported […]

2008
PMCID: 2630964
PMID: 19061486
DOI: 10.1186/1471-2105-9-521

[…] file names and options we used are listed. in 'structural?' column, 'yes' indicates structural rna sequence alignment program, and 'no' represents non-structural sequence alignment program. rnaz 1.0 with a default setting was applied to the alignments provided by mafft and clustalw. (*) dynalign version 4.5 (with m = -99) was used for the alignment quality benchmark, and dynalign […]


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RNAz in publications

 (91)
PMCID: 5913331
PMID: 29719549
DOI: 10.3389/fgene.2018.00124

[…] available in supplementary datasheet ., we created a docker container (v1.12.6) based on opensuse 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 […]

PMCID: 5814974
PMID: 29325030
DOI: 10.1093/gbe/evx273

[…] display the locations of base-paired nucleotides along each genome, were plotted with the r4rna package for r (; )., the conservation of rna secondary structure within each data set was tested using rnaz () by calculating the structure conservation index (sci). an sci = 0 indicates that rnaalifold did not find a consensus structure, whereas a sci ≈ 1 reflects a set of perfectly conserved […]

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

[…] application to ncrna discovery. however, these methods are still too slow to perform an all-against-all scan of all windows from genomic sequences., examples of the align-then-fold algorithms are rnaz [], evofold [] and petfold []. while these methods are fast and deliver accurate results, they also require that the input sequences have been aligned correctly. because these methods rely […]

PMCID: 5727441
PMID: 29069514
DOI: 10.1093/nar/gkx982

[…] further processed to contain only a single sequence per species, the one most similar to the mouse canonical isoform. this resulted in a final set of 131 mrna sequences (), which was searched using rnaz v2.1 (). the algorithm of rnaz can process at most 6 sequences. to avoid biasing our analysis toward any particular species in the alignment, we ran 200 iterations in which six species […]

PMCID: 5640933
PMID: 29029611
DOI: 10.1186/s12864-017-4171-y

[…] elements that are only poorly conserved at the nucleotide level []. as a result, some successful computational search strategies for structured ncrna candidates use algorithms such as qrna [], rnaz [], or cmfinder [], which search for nucleotide covariation or other evidence of structure formation and conservation, rather than just searching for conserved sequence. a computational search […]


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RNAz institution(s)
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany; Institute for Theoretical Chemistry, University of Vienna, Wien, Austria; European Molecular Biology Laboratory – European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK
RNAz funding source(s)
Funded, in part, by the Austrian GEN-AU projects “bioinformatics integration network III” and “noncoding RNA II”, the University of Vienna and the German Research Foundation (grants STA 850/7-1 under the auspices of SPP-1258 “Sensory and Regulatory RNAs in Prokaryotes”).

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