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. 2006 Jul 1;34(Web Server issue):W423-8.
doi: 10.1093/nar/gkl231.

RNAMST: efficient and flexible approach for identifying RNA structural homologs

Tzu-Hao Chang  1 , Hsien-Da Huang, Tzu-Neng Chuang, Dray-Ming Shien, Jorng-Tzong Horng
Affiliations

RNAMST: efficient and flexible approach for identifying RNA structural homologs

Tzu-Hao Chang et al. Nucleic Acids Res. .

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/.

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Figures

Figure 1
Figure 1
Search process of RNAMST. The figure shows how RNAMST searches a specified RNA structural motif in the given RNA sequences.
Figure 2
Figure 2
Performance comparison for RNABOB, RNAMotif and RNAMST. Search time of RNABOB, RNAMotif and RNAMST against the different search sequence databases with the IRE motif.
Figure 3
Figure 3
Performance comparison for RNABOB, RNAMotif and RNAMST. Search time of RNABOB, RNAMotif and RNAMST for the different search sequence databases with purine riboswitch motifs.
Figure 4
Figure 4
Web interface of RNAMST.
See this image and copyright information in PMC

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