RNAMST: efficient and flexible approach for identifying RNA structural homologs

RNA molecules fold into characteristic secondary structures for their diverse functional activities such as post-translational regulation of gene expression. Searching homologs of a pre-defined RNA structural motif, which may be a known functional element or a putative RNA structural motif, can provide useful information for deciphering RNA regulatory mechanisms. Since searching for the RNA structural homologs among the numerous RNA sequences is extremely time-consuming, this work develops a data preprocessing strategy to enhance the search efficiency and presents RNAMST, which is an efficient and flexible web server for rapidly identifying homologs of a pre-defined RNA structural motif among numerous RNA sequences. Intuitive user interface are provided on the web server to facilitate the predictive analysis. By comparing the proposed web server to other tools developed previously, RNAMST performs remarkably more efficiently and provides more effective and flexible functions. RNAMST is now available on the web at .

[1]  S. Gygi,et al.  Correlation between Protein and mRNA Abundance in Yeast , 1999, Molecular and Cellular Biology.

[2]  M. Hentze,et al.  Molecular control of vertebrate iron metabolism: mRNA-based regulatory circuits operated by iron, nitric oxide, and oxidative stress. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Thomas Dandekar,et al.  Riboswitch finder tool for identification of riboswitch RNAs , 2004, Nucleic Acids Res..

[4]  Jeffrey E. Barrick,et al.  Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria , 2003, Cell.

[5]  R. Breaker,et al.  Genetic Control by Metabolite‐Binding Riboswitches , 2003, Chembiochem : a European journal of chemical biology.

[6]  Graziano Pesole,et al.  PatSearch: a program for the detection of patterns and structural motifs in nucleotide sequences , 2003, Nucleic Acids Res..

[7]  Sean R. Eddy,et al.  Rfam: annotating non-coding RNAs in complete genomes , 2004, Nucleic Acids Res..

[8]  N. Gray,et al.  Control of translation initiation in animals. , 1998, Annual review of cell and developmental biology.

[9]  D. Ecker,et al.  RNAMotif, an RNA secondary structure definition and search algorithm. , 2001, Nucleic acids research.

[10]  C. Gissi,et al.  Untranslated regions of mRNAs , 2002, Genome Biology.

[11]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[12]  Graziano Pesole,et al.  UTRdb and UTRsite: a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs , 2004, Nucleic Acids Res..

[13]  G. Soukup,et al.  Riboswitches exert genetic control through metabolite-induced conformational change. , 2004, Current opinion in structural biology.

[14]  G. Benson,et al.  Tandem repeats finder: a program to analyze DNA sequences. , 1999, Nucleic acids research.

[15]  Peter Schattner,et al.  The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs , 2005, Nucleic Acids Res..

[16]  A. Viari,et al.  Palingol: a declarative programming language to describe nucleic acids' secondary structures and to scan sequence database. , 1996, Nucleic acids research.

[17]  Jeffrey E. Barrick,et al.  New RNA motifs suggest an expanded scope for riboswitches in bacterial genetic control. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[18]  S. Eddy.  Computational Genomics of Noncoding RNA Genes , 2002, Cell.

[19]  G. Steger,et al.  RNA structure and the regulation of gene expression , 1996, Plant Molecular Biology.

[20]  N. Gray,et al.  Regulation of protein synthesis by mRNA structure , 1994, Molecular Biology Reports.