GRAT--genome-scale rapid alignment tool

Modern alignment methods designed to work rapidly and efficiently with large datasets often do so at the cost of method sensitivity. To overcome this, we have developed a novel alignment program, GRAT, built to accurately align short, highly similar DNA sequences. The program runs rapidly and requires no more memory and CPU power than a desktop computer. In addition, specificity is ensured by statistically separating the true alignments from spurious matches using phred quality values. An efficient separation is especially important when searching large datasets and whenever there are repeats present in the dataset. Results are superior in comparison to widely used existing software, and analysis of two large genomic datasets show the usefulness and scalability of the algorithm.     

Navigating the applet-browser divide

The World Wide Web has emerged as a new application-delivery platform. In response, developers are offering users sophisticated Web-based Java applets that range from cybershopping carts to complex tools for genome mapping. These applets give you application functionality without taking up space on your hard drive. But trailing behind the applet bounty are new usability questions. A major one is how to make applet navigation seamless in the Web browser domain. Java applets are programs you write in Java and integrate into your Web page. Although applets can provide functionality similar to traditional applications, the applet code need not be installed on the users' hard drive. Instead, the applets execute Java-compatible Web browsers. Unlike standard Web pages, which users simply visit and browse, applet-enhanced pages let the user manipulate applet components and dynamically interact with information. The author discusses tools, techniques and concepts to optimize user interfaces