RNAMST: efficient and flexible approach for identifying RNA structural homologs

Open Access

1 July 2006

journal article
research article
Published by Oxford University Press (OUP) in Nucleic Acids Research

Vol. 34 (Web Server) , W423-W428
https://doi.org/10.1093/nar/gkl231

Abstract

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 http://bioinfo.csie.ncu.edu.tw/~rnamst/.

Keywords

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