DNA at it’s heart is enormous chunks of information. The genome of an organism like yeast, mice or humans contains an ocean of data. Currently there are several on-line genomic databases, a great example being SGD dedicated to the yeast S. cerevisiae. SGD has become a necessary tool for life-scientist over the past 10 years but at the same time has not kept up with information technology, resulting in a platform which works like a 10 year old website.
Above we see a typical SGD search, it takes 5 windows to arrive at the sequence data of 1 gene. Nevertheless, SGD is used by drug companies trying to find the next big hit, academic labs trying to cure cancer and field biologists studying wildlife.
DNA is extracted and placed through a sequencing machine which spits out the information into a computer file. Just as having an aged internet browser affects our productivity the browser one uses to view these files can have a large impact. Following the web-browser analogy we take a look at 3 different sequence browsers, starting with Vector NTI.
Vector NTI is well established and often bundled with hardware. It has many features but can often seem like information overload, causing most users to stumble through it’s many menus and windows. A step up in usability comes from the third-party software suite Sequencher, popular amongst mac users.
Sequencher strikes a healthy balance between features and usability. But is a fairly resource intensive program requiring CDs and hard drive space to store local algorithms. However, the most up to date browser is likely to be the free and light download, 4Peaks.
4Peaks allows the user to go in, read their sequence file and get out. What it lacks in features it makes up for in simplicity. The end result of any software or database is to help researchers wade through all this information and continue their studies. In this environment services such as GENEART offers to perform much of the genomic related leg work on a given project.
These are all tools, the databases, browsers and services, which enable researchers to answer the questions that line our horizon. The progress of our tools has always directly correlated with our advancement, the life sciences adoption of information technology is a necessity as we discover so much of life is condensed data in every nook.
One response to “Library of Life: Genomic Databases & Browsers”
Great writeup. Thanks.