Good Vibrations; Annotation Illustration; Speedy Sequencing

Gadget Watch | Good Vibrations Courtesy of Bel-Art Products Who hasn't experienced this frustration: When measuring out a minute quantity of a precious reagent in the microgram balance, your hand slips, and whoops! You've just dumped--and possibly lost--way more powder than you need. The Quaver® nonmotorized vibrating spatula and its nimbler sibling, the Quaverette®, could make such problems things of the past. Manufactured by Bel-Art Products (www.bel-art.com) of Pequannock, NJ, the Quaver and Quaverette purport to improve upon standard powder-dispensing practices. Instead of shaking the spatula over a weighing dish to measure out a powder, the Quaver and Quaverette feature small, toothed thumbwheels that vibrate the devices to control more effectively how much reagent is used. The two products differ slightly in length (the Quaver measures 19 cm; the Quaverette, 21 cm) and in geometry: The Quaver is a standard, curved spatula, while the Quaverette features a narrow, V-shaped blade for use with small-mouthed containers and tight corners. Both devices are available with either a stainless steel blade, or with a brown, Fluo-Kem® Teflon® coating. The spatulas are packed 24 to a case for about $25 (US) for the Quaver and $30 for the Quaverette. --Jeffrey M. Perkel Software Watch | Annotation Illustration Click for full version (23K) Visual examination of sequence database records can be a drag. Finding a single region isn't particularly difficult, but identifying multiple regions of interest--say intron and exon boundaries--is. "A picture is worth a thousand words," says Zhenjun Hu, research associate in bioinformatics, Boston University. His solution: SeqVISTA, a sequence feature visualization tool1 (zlab.bu.edu/SeqVISTA). To load a sequence into the viewer, users either enter the accession number in the application, or, while viewing a database record in Internet Explorer, click a button to load that sequence directly. The program then displays a graphical map of every sequence annotation, which can be exported as a high-resolution JPEG file for publication. The program's plug-in architecture allows third-party sequence analysis software to run from, and be visualized in, SeqVISTA. Coding a plug-in is relatively simple, says Hu, requiring about 100 lines of Java code, and several already exist, for RepeatMasker and GenScan, for example. SeqVISTA can display the results of several analyses simultaneously, facilitating direct comparisons. Project leader Zhiping Weng, assistant professor, biomedical engineering and bioinformatics, Boston University, says she hopes SeqVISTA will become a common graphical front-end for sequence analysis applications, freeing bioinformatics researchers to focus on their algorithms, rather than on a user interface. --Jeffrey M. Perkel 1. Z. Hu et al., "SeqVISTA: A graphical tool for sequence feature visualization and comparison," BMC Bioinformatics, 4:1, Jan. 4, 2003. Patent Watch | Speedy Sequencing Erica P. Johnson As the classical Sanger sequencing method takes from one to three days to read a few hundred bases, several groups have tried to improve upon the technique. One fluorescence-based alternative sequences a single nucleic acid molecule tethered to a single particle, using an exonuclease to remove the fluorescent dyes as strand synthesis proceeds. For various technical reasons, however, this approach has proven impractical. A new US patent, held by Molecular Machines & Industries of Heidelberg, Germany, describes a method designed to overcome these disadvantages and speed up sequencing.1 The patent describes a step-wise sequencing procedure in which a laser beam is focused onto an individual single-stranded nucleic acid (DNA or RNA) that has been immobilized on a planar surface. In the "preferred embodiment" of the method, the sequence is read out by addition of a polymerase and then, sequentially, solutions containing one labeled nucleotide each--that is, first A, then C, and so on. As the enzyme incorporates each new building block into the newly synthesized strand, the laser identifies the base and then "deletes" the label either by photobleaching or by photocleavage before the process repeats. --Ivan Oransky 1. S. Seeger, "Method for DNA- or RNA-sequencing," US patent 6,524,829, issued Feb. 25, 2003.

Good Vibrations; Annotation Illustration; Speedy Sequencing

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