Dataset Information

PtRNApred: computational identification and classification of post-transcriptional RNA.

ABSTRACT:

Unlabelled

Non-coding RNAs (ncRNAs) are known to play important functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as classification tools, offer a fast and reliable way for such screening and multiple classifiers have already been developed to predict well-defined subfamilies of RNA. So far, however, out of all the ncRNAs, only tRNA, miRNA and snoRNA can be predicted with a satisfying sensitivity and specificity. We here present ptRNApred, a tool to detect and classify subclasses of non-coding RNA that are involved in the regulation of post-transcriptional modifications or DNA replication, which we here call post-transcriptional RNA (ptRNA). It (i) detects RNA sequences coding for post-transcriptional RNA 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.

Availability

The ptRNApred software is open for public use on http://www.ptrnapred.org/.

SUBMITTER: Gupta Y

PROVIDER: S-EPMC4267668 | biostudies-literature | 2014 Dec

REPOSITORIES: biostudies-literature

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Publications

ptRNApred: computational identification and classification of post-transcriptional RNA.

Gupta Yask Y Witte Mareike M Möller Steffen S Ludwig Ralf J RJ Restle Tobias T Zillikens Detlef D Ibrahim Saleh M SM

Nucleic acids research 20141010 22

<h4>Unlabelled</h4>Non-coding RNAs (ncRNAs) are known to play important functional roles in the cell. However, their identification and recognition in genomic sequences remains challenging. In silico methods, such as classification tools, offer a fast and reliable way for such screening and multiple classifiers have already been developed to predict well-defined subfamilies of RNA. So far, however, out of all the ncRNAs, only tRNA, miRNA and snoRNA can be predicted with a satisfying sensitivity ...[more]

PMID: 25303994

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