Alignment Settings

Opens the Alignment Settings dialog box on which you can view the settings for the currently loaded alignment project.

Database Settings

Opens the Database Setting dialog box which you can use to view and if necessary, modify the current settings for your mySQL database.

Query Reference Tracks

Applicable only for Preloaded Reference projects and human GenBank files with NC-accession numbers. To use the Query Reference Tracks option, you must first use the Reference & Track Manager tool to download and import a database as a track into NextGENe. (You can then use the Query Reference Tracks option to load data from the track for the project that is currently opened in the viewer.

Pathway Studio Settings

Elsevier R & D Solutions Pathway Studio® uses a knowledge base of biological relationships culled from millions of articles and abstracts as well as clinical trials to enable the analysis and visualization of disease mechanisms, gene expression and proteomics and metabolomics data by researchers. A separate subscription to Pathway Studio is required to access Pathway Studio from NextGENe. If you intend to use this integration function, then you must select the appropriate access option to Pathway Studio. Three options are available and your subscription determines your selection:

Set Preferred Transcripts

Define the preferred transcripts specifically for the project that is currently opened in the viewer. The Annotation and Reference folders are not affected. The preferred transcripts are specified in a text file. The text file lists the transcripts with a single transcript (NM number) per line. See Set Preferred Transcript.