A Computational Approach to Finding RNA Tertiary Motifs in Genomic Sequences

@article{Byron2013ACA,
  title={A Computational Approach to Finding RNA Tertiary Motifs in Genomic Sequences},
  author={Kevin Byron and Jason Tsong-Li Wang},
  journal={Recent patents on DNA \& gene sequences},
  year={2013},
  volume={7 2},
  pages={
          115-22
        }
}
  • K. Byron, J. Wang
  • Published 31 July 2013
  • Biology
  • Recent patents on DNA & gene sequences
Motif finding in DNA, RNA and proteins plays an important role in life science research. Recent patents concerning motif finding in biomolecular data are recorded in the DNA Patent Database which serves as a resource for policy makers and members of the general public interested in fields like genomics, genetics and biotechnology. In this paper, we present a computational approach to mining for RNA tertiary motifs in genomic sequences. Specifically, we describe a method, named CSminer, and show… 
View on PubMed
arxiv.org
2 Citations

Figures and Tables from this paper

2 Citations

CHSalign: A Web Server That Builds upon Junction-Explorer and RNAJAG for Pairwise Alignment of RNA Secondary Structures with Coaxial Helical Stacking

TLDR
Experimental results demonstrate that CHSalign can align two RNA secondary structures containing CHS motifs more accurately than other RNA secondary structure alignment tools.

A data science approach to pattern discovery in complex structures with applications in bioinformatics

References

SHOWING 1-10 OF 70 REFERENCES

Annotation of tertiary interactions in RNA structures reveals variations and correlations.

TLDR
A comprehensively analyzed data set of 54 high-resolution RNA crystal structures reveals the diversity and variety of A-minor motif interactions and the various possible loop-loop receptor interactions that expand upon the tetraloop-tetraloop receptor.

The building blocks and motifs of RNA architecture.

Sequence to Structure (S2S): display, manipulate and interconnect RNA data from sequence to structure

TLDR
Sequence to Structure (S2S) proposes a framework in which an user can easily display, manipulate and interconnect heterogeneous RNA data, such as multiple sequence alignments, secondary and tertiary structures.

Analysis of four-way junctions in RNA structures.

The ever-growing complexity of nucleic acids: from small DNA and RNA motifs to large molecular assemblies and machines.

Emerging structural themes in large RNA molecules.

Tertiary motifs revealed in analyses of higher-order RNA junctions.

Predicting coaxial helical stacking in RNA junctions

TLDR
A computational method to predict, at the secondary structure level, the coaxial helical stacking arrangement in junctions, as well as classify the junction topology, using a data mining approach known as random forests.

Structure of the 30S ribosomal subunit

TLDR
The crystal structure of the 30S subunit from Thermus thermophilus, refined to 3 Å resolution, is reported, which will facilitate the interpretation in molecular terms of lower resolution structural data on several functional states of the ribosome from electron microscopy and crystallography.

Thermodynamics of three-way multibranch loops in RNA.

TLDR
Systems in which two strands combine to form three-way junctions were used to measure the stabilities of RNA multibranch loops by UV optical melting and isothermal titration calorimetry, and the free energy increment was calculated on the basis of a nearest neighbor model for secondary structure stability.
...