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). www.appliedbiosystems.com 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 www.appliedbiosystems.com 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