RNATOPS: Search Genomes for RNA Pseudoknots


Overview

RNATOPS (RNA via Tree decOmPoSition) is a profile based RNA structure search program that can detect RNA pseudoknots in genomes. The model for profiling the consensus structure of an RNA family is a conformational graph that specifies the topology of the consensus fold and relationship among helices and unpaired loops. Individual helices and loops are modeled with a restricted Covariance Model and profile HMM, respectively. The fold topology, helices, and loops are trained with an input pasta file that contains a multiple structural alignment for a set of training RNA sequences.


Download

RNATOPS is coded in C++ and compiled and tested on several systems, including Desktop Linux computers, a Linux cluster, and a SUN workstation running SunOS 5.1. The following downloadable versions are for Linux platforms.

  • rnatops.v1.0.zip The first version of RNATOPS that does not contain the function for automatic filter selection, for which filtering step and the whole structure search step need to be manually combined. Released June, 2008. [README file]
  • rnatops.v1.1.zip An improved version of rnatops with the automatic HMM filter selection function, for which the filtering step and the whole structure search step need to be manually combined. Released August 2008. [README file]
  • rnatops.v1.2.zip The enhanced version of rnatops with the automatic HMM filter selection, filtering, and whole structure search done in a single step. Released August, 2008, slightly after RNATOPS-W went online. [README file]


Related Software

RNATOPS-W: This is a web server version of RNATOPS (based on rnatops.v1.1). It incorporates a filtering function for search speed-up and comes with the options of automatic (HMM) filter selection and manual filter selection by the user.


Citation

    [Huang, et al., 2008] Huang, Z., Wu, Y., Robertson, J., Feng, L., Malmberg, R., and Cai, L. (2008) Fast and accurate search for non-coding RNA pseudoknot structures in genomes, Bioinforamtics, 24(20):2281-2287.

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