RNAcode

[…] mrna annotation. we discarded annotated gencode-v19 pseudogene transcripts. to remove potential protein/peptide-coding transcripts, we estimated transcript protein-coding capability using rnacode [] and cpc []. we adjusted the criteria for the output of the protein-coding potential estimation pipeline (rnacode score <18, cpc score <1.6) by analyzing well-known lncrnas […]

[…] peptide sequences were then matched against testes proteomic datasets from the mv2-25 line of d. pseudoobscura, the susa6 line of d. ps. bogotana, and hybrid crosses between the two subspecies., rnacode v0.3 was used to identify signatures of orf conservation using both the ucsc 15-species drosophila and two iterations of the pseudobase d. pseudoobscura subgroup multiple genome alignments (p […]

[…] (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 a window 3 kb up- and downstream of the srna locus were extracted […]

[…] 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 […]

[…] we hypothesized that these sequences could be a rich source of putative novel protein families.figure 1 , to predict protein-coding sequences in the unannotated fraction, we based our strategy on rnacode, a gene predictor that evaluates multiple sequence alignments using a ka/ks-based evolutionary model to distinguish between coding and non-coding sequences. in short (see methods […]

[…] of similar sequence regions by using blast [], and filtering to remove clusters matching known ncrnas present in rfam [] or to remove those with extensive protein-coding potential by using rnacode []. this process yielded many “pre-candidate” motifs that required further analysis to assess their relative likelihoods of functioning as common fungal ncrnas. each pre-candidate […]

[…] 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, […]