SeqScape™ Software for Variant Identification and SNP Discovery Applications PRODUCT BULLETIN

PRODUCT BULLETIN
Automated Sequencing
SeqScape™ Software for
Variant Identification and
SNP Discovery Applications
• Integrated basecalling, sequence
assembly, alignment and comparison for comparative sequencing
analysis
• New pairwise and multiple
sequence comparison algorithms
for fast data analysis
ABI
PRISM®
DNA
Sequencers
Basecalling
&
feature
assignment
Sample
files
Filtering
Assembly
• Simultaneous viewing of multiple
sequences and electropherograms
for easy editing
• Designed for ABI PRISM® DNA
sequencing systems
Introduction
The advent of automated sequencing
technology allows researchers to
routinely perform comparativesequencing applications such as
SNP discovery and mutation detection. Existing software tools are not
designed to address the needs of
comparative sequencing. Many
researchers routinely use two to three
software tools to complete a single
comparative sequencing project.
Applied Biosystems SeqScape software, specifically developed for
automated variant detection at the
sequence level, analyzes data
generated from automated DNA
sequencers and accurately characterizes variant sites using a single
software product.
SeqScape software is a Windows NT®based software program containing
fully integrated basecalling, sequence
assembly, alignment, and sequence
comparison tools for fast sequence
comparisons and accurate variant
identifications. SeqScape software’s
workflow design provides the needed
Report
&
export
Post-run
analysis &
editing
Comparison
Alignment
Text-based
sequences
Figure 1: SeqScape Software Workflow.
flexibility for analysis pre-configuration
and fast editing—from basecalls to
final sequence consensus. The novel
assembly and alignment algorithms
and pairwise multiple sequence
comparison algorithms are specifically
designed to provide very fast multiple
sequence analysis. In addition,
the data analysis process is fully
automated: A single mouse-click
completes a full analysis, from
sequence data to detailed reports
containing sample identities, mutation
types, amino acid changes, variant
frequencies, and annotations.
Integrated Comparative Sequencing
Analysis
Figure 1 shows SeqScape software
workflow design for a complete
analysis:
• Basecalling
• Factura™ software based feature
assignments
• Data filtering
• Sequence assembly
• Sequence alignment
• Sequence comparison
• Report generation
Users can input text-based
sequences for alignment and comparisons with other sequence data. This
allows users to conveniently compare
analyzed sequences to known
sequences imported from various
sources, including publicly available
databases such as GenBank.
PRODUCT BULLETIN
SeqScape Software Workflow
Synopsis
1. Analysis Pre-Configuration
The user can set up a project template and send reference sequence
data into a reference data group
before executing an automated
analysis.
• The user pre-configures a project
template containing all automated
settings to direct a complete
SeqScape software analysis. The
project templates are reusable,
exportable, and importable.
Figure 2. Alignment view showing specimen identities and associated base changes.
• A reference data group (RDG)
contains information such as a
reference sequence and a table
of known nucleotide variants. The
RDG is a flexible tool that allows
users to import reference
sequences and tables of associated
variants for use in analyses.
2. Fast Data Analysis
Figure 3. Simultaneous display of multiple sequences and corresponding electropherograms.
SeqScape software launches analysis
with a single mouse-click. The software basecalls all sample data,
assigns sequence features, and filters
subsequent results to ensure that
poor quality data is not passed down
the analysis pipeline. The software
then assembles data in each project
specimen and generates a consensus
sequence using novel SeqScape software algorithms. The system aligns
consensus sequences to a known
reference and compares them to
each other, to the reference, and to
the table of known mutations. After
users complete their analysis, they
can view the variants, nucleotides,
and amino acid alignments, as well
as the specimen and sample
sequence relationships using the
alignment view (Figure 2).
3. Easy Editing
Users can conveniently view and edit
each assembled specimen and the
corresponding electropherogram
(Figure 3).
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The data in the reports is hyperlinked
to the primary sequence data in the
underlying project. Users can review
and edit the data in the reports while
seeing the primary data from which
the nucleotide or amino acid variants
were identified. Editing analyzed
results automatically triggers a complete downstream analysis. The user
can quickly eliminate questionable
variant assignments and produce
updated reports.
4. Multiple Report Generation
SeqScape software automatically
generates a set of four reports for
each analysis:
• An analysis report
• A nucleotide variants report
• An amino acid variants report
• A specimen report
As shown in Figure 4, the analysis
report provides an overview of all
samples. The SeqScape Software
Quality Metrics system allows users to
quickly pinpoint samples that failed
any portion of the SeqScape software
analysis pipeline. All the variants are
also linked back to the primary data
for convenient editing and detailed
examinations. The specimen report
provides the user with a complete
analysis summary. These reports are
also printable and exportable.
Summary
• SeqScape software is a fully integrated software tool designed for
a variety of sequence comparison
and variant identification
applications.
• The algorithms are designed
and optimized for comparative
sequencing analysis.
• Data filtering and results reporting
are fully automatic.
Figure 4. Analysis report.
Specifications
Ordering Information
Algorithms and Features
Description
• ABI basecalling algorithms
P/N
SeqScape software
initial install license
4327091
• SeqScape assembly and alignment
algorithms
SeqScape software with
Sequencing Analysis Software
4327093
• SeqScape pairwise and multiple
sequence comparison algorithms
4327098
Sequence Navigator®
software to SeqScape software upgrade
• Factura™ algorithms
• SeqScape quality metrics system
File Input Format
• ABIF samples files
Please contact your local Applied
Biosystems representative for
additional ordering information.
• FASTA formatted text sequences
File output format
• Tab-delimited text files
• FASTA formatted text sequences
• SeqScape software transfer file
format archives
Optimal Computer Requirements
Operating Systems
Windows NT 4.0 OS,
service pack 5
or Windows 2000
Processor speed
Memory
“Free” Disk Space
700 MHz
256 MB RAM
6 GB
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Worldwide Sales Offices
Applied Biosystems vast distribution
and service network, composed of
highly trained support and applications
personnel, reaches into 150 countries
on six continents. For international
office locations, please call the division
headquarters or refer to our Web site
at www.appliedbiosystems.com.
Applera Corporation is committed to
providing the world's leading technology
and information for life scientists.
Applera Corporation consists of
the Applied Biosystems and
Celera Genomics businesses.
Headquarters
850 Lincoln Centre Drive
Foster City, CA 94404 USA
Phone: 650.638.5800
Toll Free: 800.345.5224
Fax: 650.638.5884
For Research Use Only.
Not for use in diagnostic procedures.
SeqScape, Factura, and AB (Design) are trademarks and Applied Biosystems and ABI PRISM
are registered trademarks of Applera
Corporation or its subsidiaries in the US and
certain other countries.
All other trademarks are properties of their
respective owners
©2001 Applied Biosystems. All rights reserved.
Information subject to change without notice.
Printed in the USA, 6/2001, JPI
Publication 106PB06-01
www.appliedbiosystems.com