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Applied Biosystems

Sequence Scanner Software v1.0

September 2005




These release notes contain the most current set of information about Sequence Scanner Software v1.0. Please review these notes prior to installing the application.


Table of Contents:


A.  Introduction to Sequence Scanner Software v1.0

B.  Features in Sequence Scanner Software v1.0

C.  Compatible Operating Systems and Minimum Systems Requirements

D.  Installing Sequence Scanner Software v1.0

E.  Known Issues


A.  Introduction to Sequence Scanner Software v1.0

Sequence Scanner Software v1.0 allows users to view, print and export sequencing sample files generated using Applied Biosystems genetic analyzer instruments. This software will also enable users to edit bases, manually trim a sequence read and generate reports. Base calling and auto-trimming features are not supported in Sequence Scanner Software.


This software reads .ab1 files generated from ABI PRISM 310, 377, 3700 DNA Analyzer and Applied Biosystems 3100-Avant, 3100, 3130/3130xl and 3730/3730xl systems.


B.  Features in Sequence Scanner Software v1.0

Import Traces

-         Traces can be imported via drag and drop, double clicking on file and the "Import Traces" dialog.


Display Traces

-         Traces listed in a tabular format with several display categories.

-         Traces can be viewed as thumbnails.

o        Thumbnails display raw data and can be scaled uniformly or individually.

-         Traces can be sorted by a variety of categories within both the tabular or thumbnail formats.

-         Traces can be viewed individually or as a group.

o        Multiple traces can be displayed by tiling individual trace viewers in 2x2, 3x1, 2x1 and 1x2 modes.

-         Analyzed and raw data can be displayed simultaneously with the ability to nudge the raw data in either direction to align with the analyzed data.

-         Dynamic zooming by dragging the mouse over a range of interest.


Export Traces

-         Traces can be exported in .txt, .seq, .scf, jpeg, pdf, .qual, .fsta and .phd.1 file formats.

-         Traces can be exported with only the post-trim sequence information to .seq, .fsta and .qual files.


Print Traces

-         Print preview capability for traces

-         Printing of the analyzed, annotation and sequence views within traces

-         Configurable trace printout settings


Edit Traces

-         Edit, delete, insert bases with undo and redo support

-         Add or remove bases to be included in the post-trim sequence


Report Results

-         Sequence Scanner provides seven reports for the imported trace files: Quality Control, Plate, Trace Score, CRL (Continuous Read Length), CRL Distribution, QV20+, and Signal Strength.

-         Data points within the reports are hyperlinked back to the trace files to open them in the trace viewer

-         Report settings are configurable

-         Print previews are available for all reports

-         Reports can also be exported in .pdf, .html, .txt and .xls formats.


User Preferences

-         Configurable thresholds for low, medium and high Trace Scores and Continuous Read Length metrics

-         Configurable color for Quality Values, Trace Scores and Continuous Read Lengths



-         Import traces dialog will always map to the last-used folder location between sessions


C.  Compatible Operating Systems and Minimum Systems Requirements

This software is compatible with Windows 2000 OS sp4 and Windows XP OS sp2.

The minimum system requirements are 512MB RAM, 733MHz CPU, 1GB of hard disk space.  The performance improves significantly with higher configuration computers.


D.  Installing Sequence Scanner Software v1.0


1.        Download the installer from the web page by clicking on the link and then selecting "Open" or "Save" from the "File Download" dialog.

2.       If you choose to save the installer to disk, then launch the installer by either selecting "Open" in the "Download complete" dialog or double-clicking the downloaded SeqScannerInstall.exe file

3.       Follow the installation wizard's instructions to install Sequence Scanner v1.0.


E.  Known Issues


-         It has been observed under rare circumstances that an install of the Sequence Scanner software following an uninstall will fail due to an installation error.

o        If you experience this problem, simply restart your computer and repeat installation.



-         When printing traces on the HP6122 printer, the advanced printing features must be enabled for printing of multiple traces to properly print out all of the selected traces.

o        To enable the advanced printing features, open the "Properties" dialog for the printer by right-clicking on the HP6122 printer's icon within the "Print" dialog and selecting "properties". From within the dialog's "Advanced" tab, check the "Enable advanced printing features" checkbox.

-         Incomplete printing job due to insufficient paper in the printing tray (Printer HP 6122)

o        On the HP6122 printer, if a printing job is interrupted due to insufficient paper, the printout may display printing errors.

-         Later annotation and sequence pages blank during a print job with a large number (>200) of traces (Printer HP 6122)

o        On the HP6122 printer, it has been observed that the annotation and sequence pages contained no data for trace 206 and above when printing 432 trace files.


Importing Traces

-         Import of traces fails for traces that have been edited in SeqA v3.7 to delete and then re-insert a base. The result is that none the traces selected for import are displayed in the "Trace Manager".

-         In some instances, if importing of traces fails, Sequence Scanner will disallow subsequent attempts to import any of the traces from the failed import.

o        Workaround: Exit and re-launch Sequence Scanner. Repeat attempt to import traces.


Exporting Traces

-         When exporting traces to jpg or pdf formats, software errors may occur if available memory is low due to running of other applications in the background.

o        If you experience this problem, try closing out of all other applications prior to exporting traces.

-         If you attempt to export traces that have identical trace file names, the last of these traces to be exported will overwrite the previous ones. This is due to the convention of naming the export files based on the original trace file names.

o        Workaround: To avoid this, simply split the trace files with identical names into separate exports, specifying different destination folders for each export.


Editing Bases

-         Edited bases fail to convert back to uppercase when deleted and then re-inserted with the same base label.

o        Edited bases are displayed as lowercase to distinguish them from called bases. Normally, when an edited base is changed back to its original call it is again displayed as uppercase as though it was never edited. This behavior does not hold true in the case of a base deletion and then re-insertion.


Remove Traces

-         If the remove traces operation is cancelled from the "Save changes to all trace files..." dialog, the operation then has no effect on subsequent attempts for the same selection of traces if initiated from the file menu or toolbar.

o        Workaround: Reselect the traces for removal or select "Remove Traces" from the "File Tasks" menu.


Security Warning

-         On Windows XP, a security warning may be issued when launching Sequence Scanner if the firewall is enabled.  We recommend leaving the firewall enabled but selecting Unblock in the displayed warning dialog.



ABI PRISM and Applied Biosystems are registered trademarks of Applera Corporation or its subsidiaries in the US and/or certain other countries.

AB (Design), Applera and Celera Discovery Systems are trademarks of Applera Corporation or its subsidiaries in the US and/or certain other countries.

All other trademarks are the property of their respective owners.

Copyright 2005 Applied Biosystems.  All rights reserved.

September 2005