Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities.
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.


BACKGROUND
http://rna.bgsu.edu/ribostral.
Mokdad
Ali
A
Department of Chemistry and Center for Biomolecular Sciences, Bowling Green State University, OH 43403, USA. mali@bgsu.edu
Leontis
Neocles B
NB
D000465:Algorithms; D020137:Base Pair Mismatch; D020029:Base Pairing; D001483:Base Sequence; D003196:Computer Graphics; D003198:Computer Simulation; D019143:Evolution, Molecular; D021621:Imaging, Three-Dimensional / Q000379:methods*; D020407:Internet; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000648:ultrastructure; D016415:Sequence Alignment / Q000379:methods*; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D014584:User-Computer Interface
D012313:RNA