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1.  Cytoscape 2.8: new features for data integration and network visualization 
Bioinformatics  2010;27(3):431-432.
Summary: Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities. Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties.
Availability and implementation: Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL). Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org.
Contact: msmoot@ucsd.edu
doi:10.1093/bioinformatics/btq675
PMCID: PMC3031041  PMID: 21149340
2.  Visualization of near-optimal sequence alignments 
Bioinformatics (Oxford, England)  2004;20(6):953-958.
Motivation
Mathematically optimal alignments do not always properly align active site residues or well-recognized structural elements. Most near-optimal sequence alignment algorithms display alternative alignment paths, rather than the conventional residue-by-residue pairwise alignment. Typically, these methods do not provide mechanisms for finding effectively the most biologically meaningful alignment in the potentially large set of options.
Results
We have developed Web-based software that displays near optimal or alternative alignments of two protein or DNA sequences as a continuous moving picture. A WWW interface to a C++ program generates near optimal alignments, which are sent to a Java Applet, which displays them in a series of alignment frames. The Applet aligns residues so that consistently aligned regions remain at a fixed position on the display, while variable regions move. The display can be stopped to examine alignment details.
Availability
Available at http://fasta.bioch.virginia.edu/ noptalign. For source code contact the authors at wrp@virginia.edu
Contact
wrp@virginia.edu
doi:10.1093/bioinformatics/bth013
PMCID: PMC2836811  PMID: 14751975

Results 1-2 (2)