Tuesday, February 24, 2009

UNIPOP: A universal operon predictor for prokaryotic genomes

The Journal of Bioinformatics and Computational Biology has published on article on a tool called UNIPOP. The operon prediction tool uses graph theory to figure out operons by mapping areas of chromosomes that experienced less shuffling between species. Because it's not a machine learning based method, there is no retraining that has to be done for different types of organisms. But it does require multiple related genome to detect signals.

You can find the source code and results on their website.  Input is the ppt files available from NCBI (for example the all.ptt.gz file for bacterial genomes).

Identification of operons at the genome scale of prokaryotic organisms represents a key step in deciphering of their transcriptional regulation machinery, biological pathways and networks. While numerous computational methods have been shown to be effective in predicting operons for well-studied organisms such as Escherichia coli (E. coli) K12 and Bacillus subtilis (B. subtilis) 168, these methods generally do not generalize well to genomes other than the ones used to train the methods because they rely heavily on organism-specific information. Several methods have been explored to address this problem through utilizing only genomic structural information conserved across multiple organisms, but they all suffer from the issue of low prediction sensitivity. In this paper, we report a novel operon prediction method that is applicable to any prokaryotic genome with accurate prediction accuracy. The key idea of the method is to predict operons through identification of conserved gene clusters across multiple genomes and through deriving a key parameter relevant to the distribution of intergenic distances in genomes. We have implemented this method using a graph-theoretic approach, called a maximum cardinality bipartite matching algorithm. Computational results have shown that our method has higher prediction sensitivity as well as specificity than any published method. We have carried out a preliminary study on operons unique to archaea and bacteria, respectively, and derived a number of interesting new insights about operons between these two kingdoms. The software and predicted operons of 365 prokaryotic genomes are available at http://csbl.bmb.uga.edu/~dongsheng/UNIPOP.

...Read more

Monday, February 23, 2009

Nanotech based DNA sequencing to lower costs

In the new issue of Nature, Oxford Nanopore describes their new DNA sequencing technology. It doesn't require fluorescent labeling, and achieves 99.8% accuracy. They say that this technology 'could' reduce costs and speed up sequencing (that is probably dependent on how the manufacturing details work out). They claim 50 base pair per second per pore, but I haven't yet seen what they estimate maximum read length would be, or how many pores per chip they expect to make. No word yet on time to market.

You can check out the corporate web site at http://nanoporetech.com/. They are pushing this technology as a possible solution to the personal genomes projects that have been springing up recently.

The technology is a combination of biochemical components and nanotechnology. You can find a nice overview animation at YouTube.

The full animation with no voice over:

Wednesday, February 11, 2009

Flash Molecular Biology Games

Sometimes you need a little fun. If you are looking for a way to kill some time, but want to be able to justify it as 'research', here are some flash games you can find on the web for free.

Microbe Kombat
You move your mouse around to guide you microbial cells to proteins that can be eaten. Enemy cells inhabit the same space and compete for the limited food source. Cute graphics/Nice Music.
Presentation: A
Fun: B
Science: A

Microbe Arena
This is a simple round based game where you customize your character and let him fight. Basically you adjust a bunch of sliders and then hit the 'fight' button. Less of a game, and more of a toy.
Presentation: B
Fun: D
Science: C-

Microbe War
Not really biology based. You are a little ship that flies around and shoots a gun. You have a small armada that goes with you.
Presentation: B
Fun: B-
Science: F

Winner: Microbe Kombat

Is Biology the future of computing?

Computer Science is a form of applied mathematics.  All the etched silicon and electricity is simply the most convenient form to express those ideas, for the time being.  Who's to say that in the future that computers won't take more inspiration from biological sources.  Speaking at the 2009 International Solid-State Circuits Conference, Intel Fellow Mark Bohr spoke about the possibility of integrated circuit design taking design queues from neuron design.

You can read more at Venture Beat

Tuesday, February 10, 2009

Large Scale Phylogenetic Rendering

The New York Times is running an article, "Crunching the Data for the Tree of Life":
For years now researchers have sequenced DNA from thousands of species from jungles, tundras and museum drawers. They have used supercomputers to crunch the genetic data and have gleaned clues to how today ’s diversity of species evolved over the past 450 million years. There’s just one problem. They have no way to visualize it...

The article mainly concerns itself with large scale phylogenetic analysis and rendering. The kind of rendering you would do with ATV or PAUP is for small sub branches of the total tree of life. This article analogizes the goals of these programs with Google Earth, programs that can quickly deal with large scale data sets.

One of the programs mentioned is Paloverde program from UC Davis(The site mentioned in the paper seemd to be down, but you can find a Arizona mirror to download the program).  They provide a compiled binary for Mac OSX.

Another program for this type of large scale rendering is Phlyo3D that works in conjunction with Walrus, a Java3D based graph rendering platform.

Monday, February 09, 2009

Careers in Computational Biology

If you are thinking about a future working in the field of Bioinformatics and Computational Biology, Nature has an article on Careers in Systems Biology.  They interviewed Malcolm Young, CEO of e-Therapeutics, and Hiroaki Kitano, Director of Sony Computer Science Laboratories, and President of the Systems Biology Institute, Tokyo, Japan.  

Thursday, February 05, 2009

Science Daily: Cancer and Computational Biology

Science Daily has a write up on a new paper that emphasize the importance of mathematical modeling of cancer cells. The paper, On the Role of Cell Signaling Models in Cancer Research, seeks to "emphasize the role and importance of the careful mathematical/computational modeling of signaling networks for the understanding of aberrant signaling in cancer and for the development of targeted therapies".

From ScienceDaily

Biology exists in a physical world. That's a fact cancer researchers are beginning to recognize as they look to include concepts of physics and mathematics in their efforts to understand how cancer develops -- and how to stop it.

Sunday, February 01, 2009

Complete Genomics

Looks like we'll be seeing more human genome information in the near future. Complete Genomics Inc. plans to sequence 1000 genomes this year, and 20,000 in 2010. This research sounds similar to the Personal Genomes Project. It's a corporate effort, so individual researchers probably won't see the data ( visit NCBI if you want some free data ).
They plan to present the results of their initial analysis in February.

From the Newswire:

MOUNTAIN VIEW, Calif., Jan. 30 /PRNewswire/ -- Complete Genomics Inc., a newly launched, third-generation human genome sequencing company, today announced that it will release its sequencing data publically for the first time at the 10th annual Advances in Genome Biology and Technology (AGBT) meeting to be held in Marco Island, Fla., from Feb. 4-7.

Dr. Clifford Reid, chairman, president and CEO of Complete Genomics, will review the analysis results during his presentation titled: "Complete Genomics: Revolutionizing Human Genome Sequencing" on Thursday, Feb. 5, at 9:10 p.m. in the Islands Ballroom at the Marco Island Marriott Resort and Spa in Marco Island, Fla.