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Protocols

RNAcode specifications

Information


Unique identifier OMICS_05866
Name RNAcode
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for RNAcode

RNAcode citations

 (27)
library_books

GLASSgo – Automated and Reliable Detection of sRNA Homologs From a Single Input Sequence

2018
Front Genet
PMCID: 5913331
PMID: 29719549
DOI: 10.3389/fgene.2018.00124

[…] r (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) (). […]

library_books

Tracing the evolution of the heterotrimeric G protein α subunit in Metazoa

2018
BMC Evol Biol
PMCID: 5896119
PMID: 29642851
DOI: 10.1186/s12862-018-1147-8

[…] coding potential that were not similar to the parent protein sequence were investigated. For this purpose, the retrogene loci were aligned with ClustalOmega [] and coding potential was accessed with RNAcode [] probing at least four different reference species. Sequence hits were reported if the region was conserved in all Primates and contained at least one methionine as a possible initiation cod […]

library_books

Discovering viral genomes in human metagenomic data by predicting unknown protein families

2018
Sci Rep
PMCID: 5758519
PMID: 29311716
DOI: 10.1038/s41598-017-18341-7

[…] th sizes between 3 and 250 sequences, yielding a total of 13,861. Highly similar sequences, which are likely duplicate copies of the same sequence with sequence errors, are interpreted incorrectly by RNAcode as independent instances and cause poor performance. To eliminate this source of bias, we sub-clustered the MCL clusters using a single-linkage approach implemented in Perl, aggregating sequen […]

call_split

Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics

2017
BMC Genomics
PMCID: 5640933
PMID: 29029611
DOI: 10.1186/s12864-017-4171-y
call_split See protocol

[…] ent clusters. Each cluster was filtered using BLAST against the Rfam database to remove any known RNAs with parameters –m8 –W10 –e 1e–10. The resulting new candidate clusters were further filtered by RNAcode [] to remove clusters whose score is greater than 15, indicating that they are potentially protein coding. The remaining clusters were fed into CMfinder [] to predict RNA structures based on c […]

library_books

Genomic and transcriptomic analysis of the toluene degrading black yeast Cladophialophora immunda

2017
Sci Rep
PMCID: 5595782
PMID: 28900256
DOI: 10.1038/s41598-017-11807-8

[…] anscript with unknown functions. Samtools were used to process the mapped reads. Bedtools were used to look for annotation overlaps.Finally conserved coding and non-coding elements were detected with RNAcode (p-value < 0.01) and RNAz (probability P > 0.9), respectively. To this aim a multiple genomes alignment of Aspergillus niger, Aspergillus nidulans, Aspergillus fumigatus, Cladophialophora immu […]

library_books

Detection of 224 candidate structured RNAs by comparative analysis of specific subsets of intergenic regions

2017
Nucleic Acids Res
PMCID: 5737381
PMID: 28977401
DOI: 10.1093/nar/gkx699

[…] vation, and this analysis is conducted using a profile HMM model of the alignment.All 224 predicted RNA classes were compared to Rfam version 12.2 () to ensure that they are not known (see ). We used RNAcode () to find potential coding regions within all predicted RNAs. The best P-value was ∼0.001. With 224 motifs, this corresponds to an E-value of ∼0.22, which is not convincing. […]

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RNAcode institution(s)
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, UK

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