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Research Tools
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GPRM - Genetic Programming for RNA Motifs
(Department of Biological Science and Technology, National Chiao Tung University, Taiwan)
GPRM is aimed at finding common secondary structure elements, not a global alignment, in a sufficiently large family (e.g. more than 15 members) of unaligned RNA sequences.
http://bioinfo.cis.nctu.edu.tw/service/gprm/
Added: Fri Mar 23 2007, Hits: 22, Reviews: 0 Write review Cached -
RegRNA - A Regulatory RNA Motifs and Elements Finder
(Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Taiwan)
RegRNA is an integrated web server for identifying the homologs of Regulatory RNA motifs and elements against an input mRNA sequence. Both sequence homologs or structural homologs of regulatory RNA motifs can be identified.
http://regrna.mbc.nctu.edu.tw/index.html
Added: Fri Aug 04 2006, Hits: 94, Reviews: 0 Write review Cached -
RNAMST
(Department of Biological Science and Technology, Institute of Bioinformatics, National Chiao Tung University, Taiwan)
RNAMST is an efficient and flexible RNA Motif Search Tool for RNA structural homologs. RNAMST web server accepts four different kinds of input formats to facilitate user to describe a RNA structure easily. Beside, several databases are provided and have been processed by our algorithm. Therefore, the user can easily and quickly search the RNA structural homologs against the huge amount of sequences. In addition, RNAMST is able to search structure with asymmetric mispair and bulges that makes the search more comprehensive and practical. RNAMST provide a convenient interface on web. The user can step by step describe the query RNA structure, select search databases and set constraints, and the results of RNA structure homologs are displayed on the screen immediately.
http://bioinfo.csie.ncu.edu.tw/~rnamst/search.php
Added: Fri Mar 23 2007, Hits: 23, Reviews: 0 Write review Cached -
Sfold
(The Bioinformatics Center at Rensselaer and Wadsworth )
Sfold focuses on applications of prediction of target accessibility, and rational design of RNA-targeting nucleic acids. Three modules, Sirna, Soligo and Sribo, provide application tools for the design of short-interfering RNAs (siRNAs), antisense oligonucleotides (oligos), and trans-cleaving ribozymes, respectively. General folding features and output are available from the fourth module, Srna.
http://www.bioinfo.rpi.edu/applications/sfold/inde...
Added: Fri Mar 23 2007, Hits: 57, Reviews: 0 Write review Cached -
Vienna RNA Secondary Structure Prediction
(RNA stuff @ tbi.univie.ac.at)
It is a web interface to the RNAfold programm that predicts the secondary structure of a single-stranded RNA or DNA sequences.
http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi
Added: Fri Mar 23 2007, Hits: 53, Reviews: 0 Write review Cached