News
Changes in the 'Usage' and 'Overview' pages (February 20, 2009)
The usage of PseudoViewr web application for any systems is now available at 'Usage of web application for any systems' page.
Due to the change in the layout style of PsudoViewer, the 'Overview' page has been updated. - go Overview
Changes in the input formats and examples (September 24, 2008)
- '.bpseq' and '.ct' files can be used in the new version of PseudoViewer web application for any systems. - go PseudoViewer web application for any systems
- Examples of large scale structures, which are 16s rRNA structures with pseudoknots and over 1500 bases, are updated. The structure data of these structures are from Comparative RNA Web (CRW) Site (http://www.rna.ccbb.utexas.edu/). - go examples
PseudoViewer quick link (July 26, 2008)
PseudoViewer web service can be accessed by using a simple get request.
The quick link page is http://pseudoviewer.inha.ac.kr/WSPV_quickSender.asp
The get values of a structure (as 'str') and a seuqnece (as 'seq') are required. the start base number (as 'start') is optional. the start base number can be added in front of the sequence.
For example (change red and blue parts of the examples as your input data),
Query 1 :
http://pseudoviewer.inha.ac.kr/WSPV_quickSender.asp?seq=CCUUACCUCGGGUAGAGGCCCA&str=(((..[[[[)))..]]]]....
Query 2 (with start base number):
http://pseudoviewer.inha.ac.kr/WSPV_quickSender.asp?seq=CCUUACCUCGGGUAGAGGCCCA&str=(((..[[[[)))..]]]]....&start=342
Query 3 (same result as Query 2):
http://pseudoviewer.inha.ac.kr/WSPV_quickSender.asp?seq=342CCUUACCUCGGGUAGAGGCCCA&str=(((..[[[[)))..]]]]....
Query 4 (omitted sequence):
http://pseudoviewer.inha.ac.kr/WSPV_quickSender.asp?seq=342CCUUACCUCGGGUAGAG459GCCCA&str=(((..[[[[)))..]]]]....
Changes in the layout style (July 24, 2008)
- go PseudoViewer web application for any systems
PseudoViewer web service (February 01, 2006)
We present a web service and web application of PseudoViewer as well as a new visualization algorithm.
Users can visualize large-scale RNA secondary structures with pseudoknots of any type from any web browser and any operating system.
- go PseudoViewer web application for any systems
- go Usage of web application
- go Examples
The PseudoViewer web service can be integrated into other systems to visualize RNA structures. Since the PseudoViewer web service runs by exchanging XML based SOAP messages, a system developed in any programming language can use the service. Sample clients written in C# and Java can be downloaded from the web service developer'guide and download page
- go Web service developer's guide
- go Download
Loop as straight line (October 26, 2005)
A loop can be drawn either as an arc or straight line. -
go Usage,
PseudoViewer in web
Changes in save image formats (September 26,2005)
Some save image formats are added. -
go Download
Postscript format (*.eps), gif format (*.gif), png format (*.png) -
go PseudoViewer in web
Changes in usage and bug fix (February 15,2005)
The input data format is expanded to handle multiple sequences -
go Usage
Numbering position can be edited. -
go Usage
Some bugs in the input format are fixed.
Release of PseudoViewer version 2.5 (July 06, 2004)
PseudoViewer version 2.5 improves PseudoViewer2 in the
following ways:
Its algorithm is more general and powerful, in that it can visualize with fewer
support lines pseudoknots with any number of stems in crossing relation to one
another, as well as what we call twisted H-type pseudoknots. -
go Examples
It automatically identifies the topological relation of the stems, such as
adjacency, crossing, and inclusion, and visualizes the relation, which is very
useful for analyzing and predicting RNA structures and classifying RNA
pseudoknots.-
go Usage
The input data format is expanded to handle incomplete or minimum structure
data. -
go Usage
PseudoViewer2.5 allows tertiary interactions other than pseudoknots in the input
data, and visualizes them. -
go Examples
Support lines between adjacent bases outside a pseudoknot are represented as
curved lines instead of straight lines to increase the readability of the
structure by reducing edge crossings. -
go Examples
The user interface has been improved, including the development of editing
facilities for the structure data and structure drawings. -
go Usage
topological
relation window (July 06, 2004)
PseudoViewer2.5 automatically identifies the topological relation of the stems,
such as adjacency, crossing, and inclusion, and visualizes the relation in the
topological relation window. It is useful for analyzing and predicting RNA
structures and classifying RNA pseudoknots. -
go Usage
Changes in the popup menu of
the structure drawing and the structure data windows (March 25, 2004)
'Undo' and 'Redo' functions are added to the popup menu of the structure
drawing window.
-
go Usage
Several editing functions such as copy, paste, undo, and selectAll are added to
the popup menu of the structure data window. -
go Usage
Changes in file menu and
draw option (September 02, 2003)
File->Open selection -
go Usage
DrawOption->Base numbering, Additional line. -
go Usage
Pseudoknot types
that can be visualized by PseudoViewer2 have been expanded. (September 01, 2003)
PseudoViewer2 can now visualize pseudoknots of nontypical type such as
trans-acting delta ribozyme and Hepatitis delta virus. -
go Examples
Changes in the input format
and the structure data editor (March 22, 2003)
PseudoViewer2 takes as input an RNA sequence with its structure data in bracket
view, which is widely used for representing pseudoknots. -
go Usage
PseudoViewer
version 2.0 was developed. (January 20, 2003)
The time for computing the PKLoop radius was reduced
significantly. (April 20, 2002)
Bug fix:
error in finding pseudoknot start and end point was fixed. (March 15, 2002)
PseudoViewer version 1.0 was developed. (February 10, 2002)