RNATOPS-W: a web server for RNA structure searches of genomes

RNATOPS-W is a web server to search sequences for RNA secondary structures including pseudoknots. The server accepts an annotated RNA multiple structural alignment as a structural profile and genomic or other sequences to search. It is built upon RNATOPS, a command line C++ software package for the same purpose, in which filters to speed up search are manually selected. RNATOPS-W improves upon RNATOPS by adding the function of automatic selection of a hidden Markov model (HMM) filter and also a friendly user interface for selection of a substructure filter by the user. In addition, RNATOPS-W complements existing RNA secondary structure search web servers that either use built-in structure profiles or are not able to detect pseudoknots. RNATOPS-W inherits the efficiency of RNATOPS in detecting large, complex RNA structures.

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

[2]  Sean R. Eddy,et al.  RSEARCH: Finding homologs of single structured RNA sequences , 2003, BMC Bioinformatics.

[3]  Russell L. Malmberg,et al.  Fast and accurate search for non-coding RNA pseudoknot structures in genomes , 2008, Bioinform..

[4]  Sean R. Eddy,et al.  Query-Dependent Banding (QDB) for Faster RNA Similarity Searches , 2007, PLoS Comput. Biol..

[5]  Anthony K. H. Tung,et al.  ARCS: an aggregated related column scoring scheme for aligned sequences , 2006, Bioinform..

[6]  Sean R. Eddy,et al.  Rfam: an RNA family database , 2003, Nucleic Acids Res..

[7]  S. Eddy,et al.  Computational identification of noncoding RNAs in E. coli by comparative genomics , 2001, Current Biology.

[8]  Zasha Weinberg,et al.  Sequence-based heuristics for faster annotation of non-coding RNA families , 2006, Bioinform..

[9]  Peter F Stadler,et al.  Fast and reliable prediction of noncoding RNAs , 2005, Proc. Natl. Acad. Sci. USA.

[10]  Russell L. Malmberg,et al.  Tree decomposition based fast search of RNA structures including pseudoknots in genomes , 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

[11]  Elena Rivas,et al.  Noncoding RNA gene detection using comparative sequence analysis , 2001, BMC Bioinformatics.

[12]  B. Haas,et al.  Searching Genomes for Noncoding RNA Using FastR , 2005, TCBB.

[13]  Mona Singh,et al.  Predicting functionally important residues from sequence conservation , 2007, Bioinform..

[14]  Sonja J. Prohaska,et al.  RNAs everywhere: genome-wide annotation of structured RNAs. , 2007, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[15]  Zasha Weinberg,et al.  Exploiting conserved structure for faster annotation of non-coding RNAs without loss of accuracy , 2004, ISMB/ECCB.

[16]  Vineet Bafna,et al.  FastR: fast database search tool for non-coding RNA , 2004, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004..

[17]  Sam Griffiths-Jones,et al.  Annotating noncoding RNA genes. , 2007, Annual review of genomics and human genetics.