RNAforester protocols

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RNAforester specifications

Information


Unique identifier OMICS_15810
Name RNAforester
Interface Web user interface
Restrictions to use None
Input data A multiple RNA sequences and structures to be aligned pairwise or multiple.
Output data A local or global aligned sequences and structures.
Programming languages C++
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Matthias Hochsmann <>

Information


Unique identifier OMICS_15810
Name RNAforester
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A multiple RNA sequences and structures to be aligned pairwise or multiple.
Output data A local or global aligned sequences and structures.
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 1.5.1
Stability Stable
Source code URL https://bibiserv.cebitec.uni-bielefeld.de/applications/rnaforester/resources/downloads/RNAforester-1.5.1-src.tar.gz
Maintained Yes

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Maintainer


  • person_outline Matthias Hochsmann <>

Publications for RNAforester

RNAforester in pipelines

 (2)
2016
PMCID: 5444242
PMID: 26984616
DOI: 10.1093/bib/bbw022

[…] effect of smoothing can be seen in . figure 2. , in 2007, we designed a plan c approach. it first computed a set of abstract consensus shapes [, ], aligned their shape representative structures with rnaforester [] and picked the best structure alignment to derive the final sequence alignment from it. aside from better speed, we hoped for a performance improvement in the dent zone. testing […]

2014
PMCID: 4041456
PMID: 24753415
DOI: 10.1093/nar/gku283

[…] using other six alignment methods, namely a sequence-only version of the needleman–wunsch, as implemented in the ‘needle’ tool from the emboss package (), locarna (), rnastrat (), rnadistance and rnaforester (both included in vienna package) and gardenia ()., we used the sum-of-pairs score (sps) () as a measure to evaluate the performances of the alignment methods. sps is defined […]


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RNAforester in publications

 (20)
PMCID: 5886760
PMID: 29409859
DOI: 10.1016/j.molp.2018.01.008

[…] pairs between rice and arabidopsis with nucleotide-resolution coverage. we calculated cds sequence identity by pairwise sequence alignment and measured in vivo rna secondary structure similarity by rnaforester, a tool that aligns rna secondary structure based on an ordered tree (, , , ). we found a significantly weak correlation between sequence identity and structure similarity (pcc = 0.08, […]

PMCID: 5444242
PMID: 26984616
DOI: 10.1093/bib/bbw022

[…] effect of smoothing can be seen in . figure 2. , in 2007, we designed a plan c approach. it first computed a set of abstract consensus shapes [, ], aligned their shape representative structures with rnaforester [] and picked the best structure alignment to derive the final sequence alignment from it. aside from better speed, we hoped for a performance improvement in the dent zone. testing […]

PMCID: 4504443
PMID: 26017195
DOI: 10.1186/s12859-015-0569-1

[…] base‐pairs, creating an extra helix which adds stability. a plausible consensus structure for the 147 variable loop members can be constructed by aligning those individual predictions, e. g. with rnaforester []. the extra helix is a bona fide feature of the trna family., in the presence of structural variation like the one described above, present‐day techniques reach a limit. family models […]

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

[…] of pseudoknot-free 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 […]

PMCID: 4244182
PMID: 25423301
DOI: 10.1371/journal.pone.0113848

[…] set of suboptimal structures of single stranded rna . the similarity of mirna structures obtained with biochemical and spectroscopic methods and anti-tn-c aptamer tn-9.6 was calculated using rnaforester ., all experiments were repeated at least three times unless otherwise stated. the products of chemical and enzymatic structure probing of mirnas were visualized with a fuji film fla 5100 […]


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RNAforester institution(s)
International Graduate School in Bioinformatics and Genome Research, University of Bielefeld, Bielefeld, Germany

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