RSEARCH

RSEARCH: finding homologs of single structured RNA sequences. BACKGROUND: For many RNA molecules, secondary structure rather than primary sequence is the evolutionarily conserved feature. No programs have yet been published that allow searching a sequence database for homologs of a single RNA molecule on the basis of secondary structure. RESULTS: We have developed a program, RSEARCH, that takes a single RNA sequence with its secondary structure and utilizes a local alignment algorithm to search a database for homologous RNAs. For this purpose, we have developed a series of base pair and single nucleotide substitution matrices for RNA sequences called RIBOSUM matrices. RSEARCH reports the statistical confidence for each hit as well as the structural alignment of the hit. We show several examples in which RSEARCH outperforms the primary sequence search programs BLAST and SSEARCH. The primary drawback of the program is that it is slow. The C code for RSEARCH is freely available from our lab’s website. CONCLUSION: RSEARCH outperforms primary sequence programs in finding homologs of structured RNA sequences.


References in zbMATH (referenced in 10 articles , 1 standard article )

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  1. Bompfünewerer, Athanasius F.; Backofen, Rolf; Bernhart, Stephan H.; Hertel, Jana; Hofacker, Ivo L.; Stadler, Peter F.; Will, Sebastian: Variations on RNA folding and alignment: Lessons from Benasque (2008)
  2. Khaladkar, Mugdha; Patel, Vandanaben; Bellofatto, Vivian; Wilusz, Jeffrey; Wang, Jason T. L.: Detecting conserved secondary structures in RNA molecules using constrained structural alignment (2008)
  3. Lladser, Manuel E.; Betterton, M. D.; Knight, Rob: Multiple pattern matching: a Markov chain approach (2008)
  4. Machado-Lima, Ariane; del Portillo, Hernando A.; Durham, Alan Mitchell: Computational methods in noncoding RNA research (2008)
  5. Sato, Kengo; Morita, Kensuke; Sakakibara, Yasubumi: PSSMTS: Position specific scoring matrices on tree structures (2008)
  6. Bauer, Markus; Klau, Gunnar W.; Reinert, Knut: Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization (2007) ioport
  7. Engelen, Stefan; Tahi, Fariza: Predicting RNA secondary structure by the comparative approach: How to select the homologous sequences (2007) ioport
  8. Song, Ying-Lei; Zhao, Ji-Zhen; Liu, Chun-Mei; Liu, Kan; Malmberg, Russell; Cai, Li-Ming: RNA structural homology search with a succinct stochastic grammar model (2005) ioport
  9. Knudsen, B.; Andersen, E. S.; Damgaard, C.; Kjems, J.; Gorodkin, J.: Evolutionary rate variation and RNA secondary structure prediction (2004)
  10. Klein, Robert J.; Eddy, Sean R.: RSEARCH: Finding homologs of single structured RNA sequences (2003) ioport