Introduction

Genomes have gotten a lot of attention lately. Large-scale sequencing methods and powerful computers have finally allowed the sequence of the human genome to be essentially completed. This milestone, though, has not been achieved in a vacuum: many other experimental systems have been fully sequenced for months or even years. Although each of these genomes are interesting and valuable in their own right, the collection of sequenced genomes is more valuable still. The quantity of data allows researchers to finally start making meaningful comparisons across genomes. Easy genome access, analysis, and comparison creates an environment in which unknown genes can be understood based on their similarity to other genes, and inter- and intra-genome sequence trends can be detected and appreciated.

Essential to this effort are computers and the software that drives the genomics effort. In order to make sense of the billions of sequenced bases, many research groups have developed their own viewers to let them visualize their own data; in the spirit of cooperation, many of these tools have been freely released to the public. Commercial interests have also started to release their own tools, some drawing on proprietary databases. The scope, power, and ease-of-use of these genome viewers varies considerably. Here we present a sampling of some of the more impressive options for viewing genomic data.

In selecting this initial set of viewers, we looked for software that allowed users to navigate the genome by either searching for a feature directly, or browsing the genome as a whole. We also selected sites that offered graphical interfaces and were accessed through the Internet, both to simplify getting started and to ensure that data were up-to-date. All viewers require an Internet connection (dedicated, high-speed is preferred, especially for long downloads); a fast processor, plenty of memory, and a large color monitor also make using these sites much more productive.

Jeff Plautz
HighWire Press

Site name: Saccharomyces Genome Database
Institution: Department of Genetics, Stanford University School of Medicine
Organism: S. cerevisiae
System requirements: Internet connection and Web browser

A very nice viewer for yeast genome data. Several map types are available (genomic and a correlated physical/genetic map). Searching was straightforward, and graphical browsing was very intuitive. Response time across the site was quite fast, and there were ample links to follow for additional information; however, some of the links for related information (literature, for example) did not have any meaningful information behind them. The site also contained a number of other sequence analysis tools for yeast research.

Site name: NCBI Map Viewer
Institution: National Center for Biotechnology Information
Organisms: Homo sapiens, Mus musculus
System requirements: Internet connection and Web browser

This viewer is brought to us from the NCBI -- the people who developed PubMed and GenBank. Data is linked extensively between the viewer and the other NCBI data sources, although it's easy to get lost in the navigation across resources, especially if your browsing takes you to a different gene or region. Vertical display of data somewhat limits the graphical field compared to other horizontal-oriented tools, so a large monitor is especially helpful here. Chromosome summary information and a full-chromosome orientation map that always appears on the screen are a few of the features that make using the graphical interface a simple experience.

Site name: Draft Human Genome Browser
Institution: University of California, Santa Cruz (Jim Kent)
Organism: Homo sapiens
System Requirements: Internet connection and Web browser

This human genome viewer offers the most different types of information diplayable on the screen at one time. Features range from predicted genes to ESTs to GC content, to name a few. There are many options for display, making the type of information as well as the window size almost completely under user control. Response time across the site is fast, although searches do tend to return a number of false positive results (often in addition to the desired result) due to the one-box-fits-all search strategy. Information beyond the viewer's display is limited to preformed searches against some NCBI databases.

Site name: The Genome Channel
Institution: Oak Ridge National Laboratory Computational Biosciences Section
Organisms: Many (> 25)
System Requirements: Internet connection and Java-capable Web browser

The Genome Channel offers more genomes in a standard viewer format than any other site we've seen. This makes comparisons between multiple genomes side-by-side (-by-side-by-side...) possible. The tool runs through a Java applet, which is generally slower than non-applet sites and can cause some problems with many common platform/browser configurations. These problems can often (but not always) be solved with some software upgrades, and the resulting product is impressive. Although the user interface isn't quite as simple as some other viewers, it works well with practice.

Site name: GeneSeen
Institution: Berkeley Drosophila Genome Project
Organism: Drosophila melanogaster
System requirements: Internet connection and Java-capable Web browser

This viewer runs through a Java applet, so it's not flawless across machines -- Mac and Linux users may experience some problems, and Windows users may also need to upgrade their software to get the viewer to work. This viewer is worth it, though. Navigation is smooth, and there is a nice correlation between the feature diagram and the cytological map of the chromosome. The large amount of genetic information can take a while to load, which can be frustrating for a user (especially on a slow connection) who is interested in a large stretch of the genome. Still, navigation is very straightforward and informative.