Posts Tagged ‘genome’

Nature Methods’s Special on Biological Visualization

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

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 […]

Presenting a genomic encyclopedia of bacteria

While sequencing the genomes of complex organisms, like humans, remains a costly and time-consuming process, simpler organisms, like bacteria, can be sequenced relatively trivially.  A new paper featured in the upcoming issue of Nature covers the results of 200 dispered organisms and shows a fascinating genomic graph of the results. A new paper takes an […]

MizBee – Multiscale Synteny Browser for Genomics

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

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 […]

Genome Visualization by the NCGR Team

In an effort to locate a genetic basis for schizophrenia, the National Center for Genome Resources (NCGR) in Santa Fe, New MExico established the Schizophrenia Genome Project.  Taking genetic data from 14 patients and 6 controls, they found themselves searching for 11,500 candidate genes amongst 16.7 billion bases.  How to find them?  Statistical analysis and […]

Visualizing Disease Genomes – Diseasome

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

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 […]