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A tool to detect and classify subclasses of non-coding RNA that are involved in the regulation of post-transcriptional modifications or DNA replication. ptRNApred (i) detects RNA sequences coding for post-transcriptional RNA (ptRNA) from the genomic sequence with an overall sensitivity of 91% and a specificity of 94% and (ii) predicts ptRNA-subclasses that exist in eukaryotes: snRNA, snoRNA, RNase P, RNase MRP, Y RNA or telomerase RNA. The tool uses an SVM based algorithm with sequence, secondary structure and thermo dynamical properties as input vectors.
An automatic annotation pipeline developed specifically for comparative genomics of small nucleolar RNAs. snoStrip makes use of sequence conservation, canonical box motifs as well as secondary structure and predicts putative targets. It embraces five parts: (i) a homology-based search procedure to accumulate potential snoRNA candidates, (ii) a post-filter that uses the conservation of box motifs and putative target sites to increase specificity, (iii) a module for extracting additional features including secondary structure and putative target predictions, (iv) the computation of family-wide alignments and (v) an optional validation check.
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