Bioinformatics Advance Access originally published online on July 4, 2006
Bioinformatics 2006 22(17):2168-2170; doi:10.1093/bioinformatics/btl360
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities
Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University OH 43403, USA
*To whom correspondence should be addressed.
Summary: RNA atomic resolution structures have revealed the existance of different families of basepair interactions, each of which with its own isosteric sub-families. Ribostral (Ribonucleic Structural Aligner) is a user-friendly framework for analyzing, evaluating and viewing RNA sequence alignments with at least one available atomic resolution structure. It is the first of its kind that makes direct and easy- to-understand superposition of the isostericity matrices of basepairs observed in the structure onto sequence alignments, easily indicating allowed and unallowed substitutions at each BP position. Potential mistakes in the alignments can then be corrected using other sequence editing software. Ribostral has been developed and tested under Windows XP, and is capable of running on any PC or MAC platform with MATLAB 7.1 (SP3) or higher installed version. A stand-alone version is also available for the PC platform.
Availability: http://rna.bgsu.edu/ribostral
Contact: mali{at}bgsu.edu
Supplementary information: A user manual is available on Ribostral website.
Received on March 30, 2006; revised on June 24, 2006; accepted on June 25, 2006
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  I. Besseova, K. Reblova, N. B. Leontis, and J. Sponer Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome Nucleic Acids Res., May 27, 2010; (2010) gkq414v1. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 P. Sharma, M. Chawla, S. Sharma, and A. Mitra On the role of Hoogsteen:Hoogsteen interactions in RNA: Ab initio investigations of structures and energies RNA, May 1, 2010; 16(5): 942 - 957. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
A. Apostolico, G. Ciriello, C. Guerra, C. E. Heitsch, C. Hsiao, and L. D. Williams Finding 3D motifs in ribosomal RNA structures Nucleic Acids Res., March 1, 2009; 37(4): e29 - e29. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Ferre, Y. Ponty, W. A. Lorenz, and P. Clote DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities Nucleic Acids Res., July 13, 2007; 35(suppl_2): W659 - W668. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Razga, J. Koca, A. Mokdad, and J. Sponer Elastic properties of ribosomal RNA building blocks: molecular dynamics of the GTPase-associated center rRNA Nucleic Acids Res., June 9, 2007; 35(12): 4007 - 4017. [Abstract] [Full Text] [PDF]
|
|