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Fingerprint related tools
 Import GeneMapper files
This tool provides an easy import for Applied Biosystems GeneMapper fragment report files. The fragment lists are imported as fingerprints into an existing fingerprint type in BioNumerics or GelCompar II, for which a metric regression (MW curve) is defined. Furthermore, the curve resolution and the band width (a cosmetic feature) can be specified.
Auto-normalize densitometric curves from sequencers
This tool performs an improved band assignment for multichannel densitometric curve files generated by automated sequencers. The channel containing the internal marker profiles produces a gel consisting of reference patterns only. In case the lanes exhibit large vertical shifts with respect to each other, the normal band assignment procedure may align some patterns out of phase.
This plugin tool provides a band assignment which performs usually better in difficult cases. Before running the script in Step 3 of the gel processing, you will need to go to Step 4 to (auto-)assign bands to the reference patterns.
If downloaded to the local computer, the script installs itself as a menu item Normalization > Auto assign (sequencer profiles).
Change fingerprint type
Automatically changes one fingerprint type into another for database entries.
Create averaged fingerprint
Creates an averaged densitometric curve from a selection of entries.
Set active zones
Tool to define the active zones on the fingerprints, i.e. the zones to include for the calculation of correlation and the calculation of band matching. Rather than graphically marking the zones as done in the fingerprint type window, this tool allows you to enter active zones as percentages of the track length. The tool is useful to reproduce exactly the same zones in different databases.
Show averaged curve
A tool to display an averaged fingerprint profile, or to display multiple profiles for a selection of entries.
Show Metrics curve
Provides a graphical preview of the metric (y-axis) plotted against the running distance (x-axis). Ths tool asks for a fingerprint type to specify. The graphical preview allows zooming in or out, copying the image to the clipboard, or printing the image.
Export metrics data of densitometric curves
This script will export the densitograms of all lanes of a gel in a tab-delimited table. Each lane is represented by two columns: (1) the metric values of all the positions (X) and (2) the corresponding densitometric values (Y).
To obtain correct results, the following conditions should be fulfilled:
- The gel lanes have to be normalized properly
- The gel should be normalized with the active reference system
- A metrics calibration curve should be present for the reference system.
Show tolerance as metric values
Provides a graphical preview of the specified position tolerance (y-axis) calculated as metric value (e.g. bp or mw) in function of the running distance (x-axis). This tool asks for a fingerprint type to specify. The graphical preview allows zooming in or out, copying the image to the clipboard, or printing the image.
Count number of bands
For a selection of entries in the database, this tool will count the number of bands each entry contains for a given fingerprint type. Before running the tool, select the entries in the database for which you want to calculate the number of bands. When the script is started, it asks the fingerprint type of choice and the output method: to a database field and/or to a tab delimited text file. If you check the database field option, the script will prompt you to select a fieldname. It suggests to create a new field for you, called "Bands in X". With X the name of the selected experiment type.
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