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1.
Figure 6

Figure 6. From: The Generic Genome Browser: A Building Block for a Model Organism System Database.

Creating a new track of targeted deletions using GBrowse.

Lincoln D. Stein, et al. Genome Res. 2002 October;12(10):1599-1610.
2.
Figure 3

Figure 3. From: The Generic Genome Browser: A Building Block for a Model Organism System Database.

A search for the term “7 transmembrane receptor.”

Lincoln D. Stein, et al. Genome Res. 2002 October;12(10):1599-1610.
3.
Figure 2

Figure 2. From: The Generic Genome Browser: A Building Block for a Model Organism System Database.

The detailed view after zooming out to 200 kb, showing semantic zooming.

Lincoln D. Stein, et al. Genome Res. 2002 October;12(10):1599-1610.
4.
Figure 4

Figure 4. From: The Generic Genome Browser: A Building Block for a Model Organism System Database.

The Generic Genome Browser is built from multiple software modules. In this illustration, modules that were not produced as part of this project are shown in a lighter color.

Lincoln D. Stein, et al. Genome Res. 2002 October;12(10):1599-1610.
5.
Figure 1

Figure 1. From: The Generic Genome Browser: A Building Block for a Model Organism System Database.

The user enters GBrowse by typing a landmark name into the text field at top. Landmarks can be gene names, clone names, accession numbers, or any other identifier configured by the administrator. Once a region is selected, it is displayed in a detailed view that summarizes annotations and other genomic features. An overview panel and a navigation bar together allow the user to move from one place to another.

Lincoln D. Stein, et al. Genome Res. 2002 October;12(10):1599-1610.
6.
Figure 5

Figure 5. From: The Generic Genome Browser: A Building Block for a Model Organism System Database.

The Bio::DB::GFF database uses a minimal schema to represent features on sequences. The main tables are fdata, which contains the position and type of each feature, fgroup, which tracks the grouping of subfeatures into features, such as high-similarity pairs in a gapped alignment, fdna, which stores the raw DNA sequence, and fattribute_to_feature, which allows attribute information to be attached to features. Attributes are used for storing such textual information as notes, synonyms, and evidence codes. The fattribute and ftype tables, respectively, hold attribute names and the method and source fields. For retrieval efficiency, the fdna table fragments each DNA into small pieces and stores the beginning of each piece in the foffset field.

Lincoln D. Stein, et al. Genome Res. 2002 October;12(10):1599-1610.

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