RNAComp: A new method for RNA secondary structure alignment

In this paper, a new algorithm for alignment of two RNA secondary structures without pseudoknots is presented. The algorithm is based on finding the longest common sub-structures between two RNA structures and special effort is devoted for aligning the beginning and the end parts of the existing stems (base pairs) in the secondary structures of two RNAs. The results of structure alignment of different types of RNA by this algorithm are obtained, and the result of this algorithm show more consistency with the models in the evolution rather than the other existing structure alignment algorithms.

[1]  G. Ruvkun,et al.  A uniform system for microRNA annotation. , 2003, RNA.

[2]  Jie Feng,et al.  A 3D graphical representation of RNA secondary structures based on chaos game representation , 2008 .

[3]  Michael R. Fellows,et al.  Algorithms and complexity for annotated sequence analysis , 1999 .

[4]  R. Nussinov,et al.  Tree graphs of RNA secondary structures and their comparisons. , 1989, Computers and biomedical research, an international journal.

[5]  Kaizhong Zhang,et al.  Identifying consensus of trees through alignment , 2000, Inf. Sci..

[6]  Na Liu,et al.  A method for rapid similarity analysis of RNA secondary structures , 2006, BMC Bioinformatics.

[7]  Nan Yu,et al.  The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs , 2002, BMC Bioinformatics.

[8]  P. Schuster,et al.  RNA multi-structure landscapes , 1993, European Biophysics Journal.

[9]  Ruth Nussinov,et al.  RNA secondary structures: comparison and determination of frequently recurring substructures by consensus , 1989, Comput. Appl. Biosci..

[10]  Christine Guthrie,et al.  Spliceosomal snRNAs Mg2+-Dependent Chemistry at the Catalytic Core? , 2002, Cell.

[11]  G. Mauri,et al.  An algorithm for finding conserved secondary structure motifs in unaligned RNA sequences , 2008, Journal of Computer Science and Technology.

[12]  Bin Ma,et al.  Computing similarity between RNA structures , 1999, Theor. Comput. Sci..

[13]  Nan Yu,et al.  The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs: Correction , 2002, BMC Bioinformatics.

[14]  Bo Liao,et al.  A 3D Graphical Representation of RNA Secondary Structures , 2004, Journal of biomolecular structure & dynamics.

[15]  Andrzej Lingas,et al.  A Fast Algorithm for Optimal Alignment between Similar Ordered Trees , 2001, CPM.

[16]  Abraham Lempel,et al.  On the Complexity of Finite Sequences , 1976, IEEE Trans. Inf. Theory.

[17]  James W. Brown.  The ribonuclease P database , 1998, Nucleic Acids Res..

[18]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[19]  Kaizhong Zhang,et al.  Comparing multiple RNA secondary structures using tree comparisons , 1990, Comput. Appl. Biosci..

[20]  R. Gutell,et al.  Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective. , 1994, Microbiological reviews.

[21]  Graziano Pesole,et al.  UTRdb and UTRsite: specialized databases of sequences and functional elements of 5' and 3' untranslated regions of eukaryotic mRNAs , 2000, Nucleic Acids Res..

[22]  Bin Ma,et al.  A General Edit Distance between RNA Structures , 2002, J. Comput. Biol..

[23]  Bruce A. Shapiro,et al.  An algorithm for comparing multiple RNA secondary structures , 1988, Comput. Appl. Biosci..

[24]  J. McCaskill.  The equilibrium partition function and base pair binding probabilities for RNA secondary structure , 1990, Biopolymers.

[25]  Kaizhong Zhang,et al.  Simple Fast Algorithms for the Editing Distance Between Trees and Related Problems , 1989, SIAM J. Comput..

[26]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

[27]  Robert Giegerich,et al.  Local similarity in RNA secondary structures , 2003, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003.

[28]  Peter F. Stadler,et al.  Alignment of RNA base pairing probability matrices , 2004, Bioinform..

[29]  T. Kiss.  Small Nucleolar RNAs An Abundant Group of Noncoding RNAs with Diverse Cellular Functions , 2002, Cell.

[30]  Tao Jiang,et al.  Alignment of Trees - An Alternative to Tree Edit , 1994, Theor. Comput. Sci..