RELEASE NOTES
Sequence Scanner™ Software 2
Sanger Sequencing Data Viewer
Copyright 2012, Life Technologies Corporation and/or its affiliate(s).
All rights reserved.
June 2012
CONTENTS:
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Software Overview
Supported Data Files
Main Functionality
Changes in Sequence Scanner™ v.2.0 as Compared to Sequence Scanner™ v.1.0
Compatible Operating Systems and PC Requirements
Installing Sequence Scanner™ Software 2
Known Issues and Limitations
SOFTWARE OVERVIEW
Sequence Scanner™ Software 2 allows users to view, print and export sequencing sample files
generated using genetic analyzer instruments by Life Technologies. This software also enables 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.
SUPPORTED DATA FILES
Sequence Scanner™ Software 2 is designed to import and view sequencing traces from the sequencing
analysis sample files (.ab1) from all currently supported genetic analyzers including 3500 series.
Sequnce Scanner™ Software 2 fully supports data generated from the following Applied Biosystems
instruments:
- Applied Biosystems 3500 Genetic Analyzer
- Applied Biosystems 3500xl Genetic Analyzer
- Applied Biosystems 3130 Genetic Analyzer
- Applied Biosystems 3130xl Genetic Analyzer
- Applied Biosystems 3730 DNA Analyzer
- Applied Biosystems 3730xl DNA Analyzer
- 310 Genetic Analyzer
Sequence Scanner™ Software 2 offers limited support for data generated on 3100 and 3700 instruments.
MAIN FUNCTIONALITY
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Import Traces
o Traces can be imported via drag and drop, double clicking on file and the "Import Traces"
dialog.
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Display Traces
o Traces listed in a tabular format with several display categories.
o Traces can be viewed as thumbnails.
o Thumbnails display raw data and can be scaled uniformly or individually.
o Traces can be sorted by a variety of categories within both the tabular or thumbnail
formats.
o 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.
o 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.
o Dynamic zooming by dragging the mouse over a range of interest.
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Export Traces
o Traces can be exported in .txt, .seq, .scf, .jpg, .pdf, .qual, .fsta and .phd.1 file formats.
o Traces can be exported with only the post-trim sequence information to .seq, .fsta and
.qual files.
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Print Traces
o Print preview capability for traces.
o Printing of the analyzed, annotation and sequence views within traces.
o Configurable trace printout settings.
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Edit Traces
o Edit, delete, insert bases with undo and redo support.
o Add or remove bases to be included in the post-trim sequence.
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Report Results
o 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.
o Data points within the reports are hyperlinked back to the trace files to open them in the
trace viewer.
o Report settings are configurable.
o Print previews are available for all reports.
o Reports can also be exported in .pdf, .html, .txt and .xls formats.
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User Preferences
o Configurable thresholds for low, medium and high Trace Scores and Continuous Read.
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Length metrics
o Configurable color for Quality Values, Trace Scores and Continuous Read Lengths.
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Miscellaneous
o Import traces dialog will always map to the last-used folder location between sessions.
CHANGES IN SEQUENCE SCANNER™ V.2.0 AS COMPARED TO SEQUENCE SCANNER™ V.1.0
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Sequence Scanner Software 2 supports Microsoft Windows® 7 Professional (32-bit) SP1
operating system.
COMPATIBLE OPERATING SYSTEMS AND PC REQUIREMENTS
1. Recommended configuration
The software can be installed, launched and run on a computer with the following specification:
 The software shall be supported on Dell OptiPlex XE Windows® 7 SP1 professional 32-bit
operating system.
 CPU: Core 2 Duo E8400/3.0GHz
 Memory: 4GB
 Disk: Free space: 1GB
2. Minimum configuration
The software can be installed, launched and run as a standalone on a computer with the following
specification: Windows® 7 Professional SP1, 32-bit
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CPU: 2GHz or faster Intel processor
Memory: 2GB
Disk: Free space: 1GB for application on the drive for the software
3. Display Requirements
 User can view all UI elements of the application on the screen without having to scroll
vertically if the software is run on a monitor with minimum 1280x1024 pixel resolution for full
screen display.
 User should use Windows® 7 default theme
NOTE: This software has been extensively tested on Windows® 7 SP1 (32-bit) version. While there are
some indications that software will run normally on the 64-bit version of Windows® 7 SP1 operating
system, the 64-bit configuration is not officially supported. It is strongly recommended that this software is
run on Windows® 7 SP1 (32-bit).
INSTALLING SEQUENCE SCANNER™ SOFTWARE 2
The user must have administrator privileges to install this application.
Insert the installation CD or access installation directory from Windows Explorer. Follow the install wizard
steps during the installation. If the launcher does not start automatically, manually click setup.exe from
Windows Explorer.
Once installation is completed, go to the Start menu. From the Start menu, go to All Programs > Applied
Biosystems > Seq Scanner 2 folder and click on the Seq Scanner 2 shortcut to start Sequence Scanner™
Software 2.
KNOWN ISSUES AND LIMITATIONS
Printing
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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 HP6122).
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 HP6122)
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
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Import of traces fails for traces that have been edited in SeqA v3.7 to delete and then re-insert a
base.
o 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
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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
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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.
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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.
Removing Traces
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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.
LEGAL DISCLAIMER AND TERMS AND CONDITIONS OF CUSTOMER
INSTALLATIONS OR USE
LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) MAKE NO REPRESENTATIONS
REGARDING SEQUENCE SCANNER™ SOFTWARE 2 USE OR PERFORMANCE AND ACCEPTS NO
LIABILITY AS A RESULT OF THE INSTALLATION OR USE OF SEQUENCE SCANNER™ SOFTWARE
2. SEQUENCE SCANNER™ SOFTWARE 2 IS PROVIDED "AS IS" AND "WITH ALL FAULTS". LIFE
TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) DISCLAIM ALL WARRANTIES
RELATING TO SEQUENCE SCANNER™ SOFTWARE 2, EXPRESS OR IMPLIED, INCLUDING THE
WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, OR NONINFRINGEMENT.
IN NO EVENT SHALL LIFE TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S) OR ITS
SUPPLIERS BE RESPONSIBLE OR LIABLE, WHETHER IN CONTRACT, TORT, WARRANTY OR
UNDER ANY STATUTE (INCLUDING WITHOUT LIMITATION ANY TRADE PRACTICE, UNFAIR
COMPETITION OR OTHER STATUTE OF SIMILAR IMPORT) OR ON ANY OTHER BASIS FOR
SPECIAL, INDIRECT, INCIDENTAL, MULTIPLE, PUNITIVE, OR CONSEQUENTIAL DAMAGES
ARISING OUT OF THE POSSESSION OR USE OF, OR THE INABILITY TO USE, SEQUENCE
SCANNER™ SOFTWARE 2 RELEASE OR DOCUMENTATION, EVEN IF LIFE TECHNOLOGIES
CORPORATION AND/OR ITS AFFILIATE(S) IS ADVISED IN ADVANCE OF THE POSSIBILITY OF
SUCH DAMAGES, INCLUDING WITHOUT LIMITATION DAMAGES ARISING FROM OR RELATED TO
LOSS OF USE, LOSS OF DATA, DOWNTIME, OR FOR LOSS OF REVENUE, PROFITS, GOODWILL
OR BUSINESS OR OTHER FINANCIAL LOSS. IN ANY CASE, THE ENTIRE LIABILITY OF LIFE
TECHNOLOGIES CORPORATION AND/OR ITS AFFILIATE(S)’ AND ITS SUPPLIERS UNDER THIS
LICENSE, OR ARISING OUT OF THE USE OF SEQUENCE SCANNER™ SOFTWARE 2 RELEASE,
SHALL NOT EXCEED IN THE AGGREGATE THE PURCHASE PRICE OF THE PRODUCT. SOME
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For Research Use Only. Not intended for animal or human therapeutic or diagnostic use.
Information in this document is subject to change without notice.
Life Technologies Corporation and/or its affiliate(s) assumes no responsibility for any errors that may
appear in this document.
Notice to Purchaser: License Disclaimer.
Purchase of this software product alone does not imply any license under any process, instrument or
other apparatus, system, composition, reagent or kit rights under patent claims owned or otherwise
controlled by Life Technologies Corporation and/or its affiliate(s), either expressly, or by estoppel.
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