RASS: a web server for RNA alignment in the joint sequence-structure space.
Comparison of ribonucleic acid (RNA) molecules is important for revealing their evolutionary relationships, predicting their functions and predicting their structures. Many methods have been developed for comparing RNAs using either sequence or three-dimensional (3D) structure (backbone geometry) information. Sequences and 3D structures contain non-overlapping sets of information that both determine RNA functions. When comparing RNA 3D structures, both types of information need to be taken into account. However, few methods compare RNA structures using both sequence and 3D structure information. Recently, we have developed a new method based on elastic shape analysis (ESA) that compares RNA molecules by combining both sequence and 3D structure information. ESA treats RNA structures as 3D curves with sequence information encoded on additional coordinates so that the alignment can be performed in the joint sequence-structure space. The similarity between two RNA molecules is quantified by a formal distance, geodesic distance. In this study, we implement a web server for the method, called RASS, to make it publicly available to research community. The web server is located at http://cloud.stat.fsu.edu/RASS/.
Department of Computer Science, Florida State University, Tallahassee, FL 32306, USA.
Gewen
G
He
Department of Statistics, Florida State University, Tallahassee, FL 32306, USA.
Albert
A
Steppi
Department of Statistics, Florida State University, Tallahassee, FL 32306, USA.
Jose
J
Laborde
Department of Statistics, Florida State University, Tallahassee, FL 32306, USA.
Anuj
A
Srivastava
Department of Computer Science, Florida State University, Tallahassee, FL 32306, USA.
Peixiang
P
Zhao
Department of Statistics, Florida State University, Tallahassee, FL 32306, USA Jinfeng@stat.fsu.edu.
Jinfeng
J
Zhang
D020407:Internet; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D016415:Sequence Alignment; D017423:Sequence Analysis, RNA; D012984:Software
D012313:RNA