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National Center For Genome Resources Releases DNA Sequence Viewing Software

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SANTA FE, NM--The National Center for Genome Resources (NCGR), a nonprofit bioinformatics organization here, has released a new Java-based software tool designed to help genomics researchers view and analyze DNA sequences. Sequence Viewer is a graphical utility that can dynamically retrieve and navigate genetic sequence data in the center's Genome Sequence Database. The free, public software is part of a suite of NCGR tools that enable researchers to access, visualize, and analyze sequence data.

A team of NCGR's technical and scientific experts designed Sequence Viewer to satisfy researchers' need for graphical representations of nucleotide sequences in the database and detailed descriptions of sequence annotation. The tool can find a region of a sequence that integrates with a gene quickly, so users don't have to search through a lengthy, complex flat-file report, NCGR said. The product also can be used as a QC tool to locate mistakes in feature position.

"Sequence Viewer is very useful for reviewing biological information associated with a sequence by providing researchers with a quick visual overview of a sequence. For most people, looking at a picture aids in understanding," remarked Carol Harger, the database's manager. "By utilizing the content cues, such as gene names, they can then hone in on a specific region of the DNA sequence to glean in-depth information."

NCGR said the display of public, continuous sequences in its database generated by Sequence Viewer can be scaled and customized, and that users can easily distinguish between features on the forward and reverse strands. The tool displays annotated biological features as bars in feature panes, which can be scrolled. Base-pair position is indicated with a ruler.

According to NCGR, other beneficial features of the software include:

* Displays of sequence and feature data in scrollable text boxes containing flat-file-like text. Information about modified bases also is accessible.

* Integration of Sequence Viewer with other database tools for search purposes. NCGR's web-based query or search tools developed for use with the database, including Ad Hoc, Excerpt, Flatfile, and Maestro, can be accessed directly from Sequence Viewer.

* Simultaneous display of multiple detailed feature text boxes, allowing users to compare data for different features.

* Visual cues representing sequence tagged sites, modified bases, incomplete ends, multiple locations, and fuzzy ends. Tool tips provide feature identification, and detailed data are available by selecting features in the map or by accessing a sortable list of features.

Sequence Viewer is available as a Java applet or a Java application. It can be accessed at NCGR's web site, at http://www.ncgr.org/gsdb/sv.

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