de.mpg.escidoc.pubman.appbase.FacesBean
English
 
Help Guide Disclaimer Contact us Login
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT

Released

Journal Article

SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments

MPS-Authors
http://pubman.mpdl.mpg.de/cone/persons/resource/persons84246

Tabei,  Y
Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons84265

Tsuda,  K
Department Empirical Inference, Max Planck Institute for Biological Cybernetics, Max Planck Society;

Locator
There are no locators available
Fulltext (public)
There are no public fulltexts available
Supplementary Material (public)
There is no public supplementary material available
Citation

Tabei, Y., Tsuda, K., Kin, T., & Asai, K. (2006). SCARNA: Fast and Accurate Structural Alignment of RNA Sequences by Matching Fixed-Length Stem Fragments. Bioinformatics, 22(14), 1723-1729. doi:10.1093/bioinformatics/btl177.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0013-D1D9-7
Abstract
The functions of non-coding RNAs are strongly related to their secondary structures, but it is known that a secondary structure prediction of a single sequence is not reliable. Therefore, we have to collect similar RNA sequences with a common secondary structure for the analyses of a new non-coding RNA without knowing the exact secondary structure itself. Therefore, the sequence comparison in searching similar RNAs should consider not only their sequence similarities but their potential secondary structures. Sankoffamp;lsquo;s algorithm predicts the common secondary structures of the sequences, but it is computationally too expensive to apply to large-scale analyses. Because we often want to compare a large number of cDNA sequences or to search similar RNAs in the whole genome sequences, much faster algorithms are required. We propose a new method of comparing RNA sequences based on the structural alignments of the fixed-length fragments of the stem candidates. The implemented software, SCARNA (Stem Candidate Aligner for RNAs), is fast enough to apply to the long sequences in the large-scale analyses. The accuracy of the alignments is better or comparable to the much slower existing algorithms.