:: DESCRIPTION
MASTR performs multiple alignment and secondary structure prediction on a set of structural RNA sequences.
::DEVELOPER
The Bioinformatics Centre , University of Copenhagen
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2007 Dec 15;23(24):3304-11. Epub 2007 Nov 15.
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing.
Lindgreen S, Gardner PP, Krogh A.
:: DESCRIPTION
BPLA kernel (Base-pairing profile local alignment) is a powerful method that evaluates the similarity between a pair of RNAs taking into account secondary structure information. Based on the accurate similarity calculated by BPLA kernel, you can perform a broad range of structural RNA analysis, including family prediction, hierarchical clustering, and remote homology search. The method is applicable not only to classical genomic screens, but also to unannotated noncoding transcripts produced by next-generation sequencing technologies (RNA-seq).
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S3. doi: 10.1186/1471-2105-11-S7-S3.
Robust and accurate prediction of noncoding RNAs from aligned sequences.
Saito Y1, Sato K, Sakakibara Y.
:: DESCRIPTION
WAR utilizes several tools simultaneously to align and predict the common secondary structure of multiple RNA sequences.
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
WAR: Webserver for aligning structural RNAs
Elfar Torarinsson and Stinus Lindgreen
Nucleic Acids Res. 2008 July 1; 36(Web Server issue): W79–W84.
:: DESCRIPTION
RNAdbtool is a collection of tools which can be used to perform semi-automated update of RNA structural databases.
::DEVELOPER
Center for non-coding RNA in Technology and Health (RTH)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2001 Jul;17(7):642-5.
Semi-automated update and cleanup of structural RNA alignment databases.
Gorodkin J, Zwieb C, Knudsen B.