RNAsalsa statistics

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Associated diseases

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RNAsalsa specifications

Information


Unique identifier OMICS_16338
Name RNAsalsa
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 0.8.1
Stability Beta
Source code URL http://software.zfmk.de/RNAsalsa_0.8.1.tar.gz
Maintained Yes

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RNAsalsa in publications

 (7)
PMCID: 4602297
PMID: 26478699
DOI: 10.3897/zookeys.523.6066

[…] and used kanakyella gentilsiana, crosseana crosseana, and crosseana melanosoma as outgroups (table ). the alignment of 16s rrna and its2 was generated using secondary structure information using rnasalsa 0.8.1 () (for details see ) and checked for ambiguous and randomly similar sites in aliscore 2.0 (). we defined seven partitions. partitionfinder 1.1.0 () identified the following scheme […]

PMCID: 4557820
PMID: 26330076
DOI: 10.1186/s12862-015-0458-2

[…] process, as embodied by the congruence methodologies., employing secondary structure for aligning sequences has, however, at least two potential drawbacks. first, since automated methods, like rnasalsa [], remain largely underappreciated, secondary structure guided alignment still relies on extremely time-consuming manual alignment. second, consensus secondary structure alignment cannot […]

PMCID: 4002437
PMID: 24777067
DOI: 10.1371/journal.pone.0095227

[…] reference sequences, the introns removed, and the alignment trimmed at both ends. the tef1alignment was adjusted by eye in seaview for four sequences. ssu was additionally aligned by structure in rnasalsa (using the structure model for coprinus cinereus reference sequence m92991, found in the european ribosomal database at http://bioinformatics.psb.ugent.be/webtools/rrna/). ribosomal genes […]

PMCID: 3585860
PMID: 23384124
DOI: 10.1186/1471-2148-13-30

[…] coding gene and the mitochondrial gene coi was carried out in mega 5 [] with muscle [] using default parameters. the ribosomal genes were aligned based on secondary structure information using rnasalsa v0.8.1 [] with apis mellifera structural data used as a constraint. weakened constraint settings (s1, s2 and s3 = 0.51) were used to preserve structural information as described by letsch […]

PMCID: 4553606
PMID: 26466539
DOI: 10.3390/insects3020473

[…] conventional approach, sequences were aligned by using muscle version 3.6 [] with default settings. the resulting alignment required moderate additional editing. in a second approach, the software rnasalsa 0.8.1 [] was used to simultaneously derive a secondary structure of the rna molecule and to obtain a structure-guided alignment. for this purpose, the secondary structure of the 16s rrna […]


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