RNAcode

[…] 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) (). […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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 […]

[…] 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. […]