Posts Tagged ‘genome’

Nature Methods’s Special on Biological Visualization

by Randall Handon March 1, 2010
The latest issue of ‘nature|methods” journal contains give special articles all about visualization of biological data. A series of five commissioned Reviews discuss the challenges of visualizing biological data and the visualization tools available to biologists working with genomes, alignments and phylogenies, macromolecular structures, images and systems biology data. The five articles are: Forward: Supplement […]

Skittle: A 2-Dimensional Genome Visualization Tool

by Randall Handon December 30, 2009
In the newest issue of BMC Bioinformatics 2009 (10:452), Josiah Seaman and John Sanford publish details for their 2-D genome visualizer called ‘Skittle’. Results: This program first creates a 2-dimensional nucleotide display by assigning four colors to the four nucleotides, and then text-wraps to a user adjustable width. This nucleotide display is accompanied by a […]

MizBee – Multiscale Synteny Browser for Genomics

by Randall Handon October 14, 2009
Biologists out there might want to take a look at the open-source MizBee visualization tool. MizBee is a multiscale synteny browser for exploring conservation relationships in comparative genomics data. Using side-by-side linked views, MizBee enables efficient data browsing across a range of scales, from the genome to the gene. The design of MizBee is grounded […]

GPGPU Accelerated Epistatis Analysis in Human Genetics

by Randall Handon July 24, 2009
Human genetics research is lengthy and slow, and one primary cause of that is the slow combinatorial algorithms used.  Researchers at Dartmouth have just published a paper where they implemented these algorithms on NVidia graphics cards with CUDA, with amazing results. One such algorithm is Multifactor Dimensionality Reduction (MDR). Expert knowledge guided evolutionary computing wrappers […]

Visualizing Disease Genomes – Diseasome

by Randall Handon July 15, 2009
A new website, Diseasome, visualizes 516 diseases and 903 genes to show common backgrounds and effects.  The result is an interactive map showing how groups of diseases, say Cancer, share a common background and genetic material but manifest in slightly different ways.  There is also a wealth of information about how they did it: Nodes […]

Symbolic Scatter Plot Helps Visualize Patterns Within DNA Sequence

by Randall Handon July 1, 2009
David Cox of North Carolina State University has created a new visualization method for DNA sequences that he’s calling “symbolic scatter plots”. His technique starts out similar to Blast, he says, in that it takes the sequence at hand and breaks it up into small words. Whereas Blast computationally plugs those words into a database […]