SeqScape Software Version 2.1 User Guide - InfoNet

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Chapter 1 Introduction to ABI PRISM SeqScape Software • New Basecallers. The KB basecaller is a new algorithm that identifies mixed or pure bases and generates sample quality values. The ABI basecaller is an algorithm used in sequencing analysis software. • Basecalling with ABI basecaller only is no longer available. In SeqScape Software v1.1, you can choose to basecall data with ABI basecaller or ABI basecaller with TraceTuner Software. In software v2.0, you do not have the option to basecall with ABI basecaller only. The new options are: – Basecall with ABI and TraceTuner software (automatic) – Basecall with KB basecaller • Implicit Reference is no longer available. In software v1.1, you can have an empty RDG and use the first specimen as your implicit reference sequence, but this is no longer available in v2.0. However, you can create an RDG and add an .ab1 sample file as a reference sequence. 1-4 ABI PRISM SeqScape Software v2.1 User Guide DRAFT August 28, 2003 2:54 pm, 1_Intro.fm
About SeqScape Software About SeqScape Software Genetic Analyzer Applications SeqScape Software Applications Resequencing Data with SeqScape Software SeqScape software is one of a suite of Applied Biosystems Genetic Analyzer software applications designed to control an instrument, collect data, and manage automated analysis. This suite of data collection and analysis software systems includes: • GeneMapper Software – Performs genotyping using fragment analysis methods. • ABI PRISM ® Sequencing Analysis Software – Displays, analyzes, edits, and prints sequencing files. • ABI PRISM ® SeqScape ® Software – Performs sequence comparisons for variants identification, SNP discovery, and SNP validation. Common resequencing applications include: • SNP discovery and validation • Mutation analysis and heterozygote identification • Sequence confirmation for mutagenesis or clone-construct confirmation studies • Identification of genotype, allele, and haplotype from a library of known sequences SeqScape software allows analysis of resequenced data, comparing consensus sequences to a known reference sequence and optionally searching against a sequence library. For example, a simple project might contain one contiguous reference sequence in a single reading frame, with no known nucleotide or amino acid variant information. SeqScape software compares a consensus sequence to this reference sequence, identifying any differences. A more complex project might include a reference sequence constructed from several reference segments representing multiple exons and introns. You can use SeqScape software to: • Build unique sequence layers composed of different groupings of reference sequence features. • Compare consensus sequences to each unique layer. • Identify differences. • Compare the sequence to a library of sequences to identify the closest match. ABI PRISM SeqScape Software v2.1 User Guide 1-5 DRAFT August 28, 2003 2:54 pm, 1_Intro.fm
Page 1 and 2: ABI PRISM ® SeqScape ® Software V
Page 3 and 4: Contents Preface How to Use This Gu
Page 5 and 6: Specifying the Analysis Settings .
Page 7 and 8: Adding Specimens and Importing Data
Page 9 and 10: Editing the Data . . . . . . . . .
Page 11 and 12: Understanding the Autoanalysis Mana
Page 13 and 14: Appendix G Software Warranty Comput
Page 15 and 16: Preface How to Use This Guide Purpo
Page 17 and 18: Conventions Used in This Guide Safe
Page 19 and 20: How to Obtain Services and Support
Page 21 and 22: Introduction to ABI PRISM SeqScape
Page 23: For Users of Earlier Versions of Se
Page 27 and 28: About SeqScape Software How the Sof
Page 29 and 30: Getting Started 2 2 This chapter co
Page 31 and 32: Hardware and Software Requirements
Page 33 and 34: SeqScape Software Versions SeqScape
Page 35 and 36: Installing the Full Version for the
Page 37 and 38: Removing SeqScape Software Removing
Page 39 and 40: Starting SeqScape Software for the
Page 49 and 50: New Users Logging In for the First
Page 51 and 52: SeqScape Software Structure Project
Page 53 and 54: SeqScape Software Toolbar The secon
Page 55 and 56: Menus on the Main SeqScape Window C
Page 57 and 58: Creating Analysis Defaults and Disp
Page 59 and 60: Analysis Defaults Settings Analysis
Page 61 and 62: Creating Analysis Protocols 5. Sele
Page 63 and 64: Creating Analysis Protocols Specify
Page 65 and 66: Creating Analysis Protocols 2. Sele
Page 67 and 68: Creating Analysis Protocols 2. Ente
Page 69 and 70: Specifying the Analysis Settings If
Page 71 and 72: Specifying the Analysis Settings 4.
Page 73 and 74: Specifying the Analysis Settings 6.
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Specifying Display Settings To spec
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Specifying Display Settings 5. Sele
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Specifying Display Settings d. To d
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Creating a Reference Data Group 4 4
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Reference Data Group (RDG) Referenc
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Reference Data Group (RDG) Download
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Creating a New RDG Using the Wizard
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Creating a New RDG Using SeqScape M
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Defining Regions of Interest (ROI)
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Defining Regions of Interest (ROI)
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ROI Tab Descriptions Columns in the
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Creating a Library Setting Up Your
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Creating a Library 8. Select a laye
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Creating New Layers The Library Edi
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Creating New Layers Adding a Refere
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Declaring Variants into an RDG Decl
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Declaring Variants into an RDG 4. I
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Declaring Variants into an RDG 6. A
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Creating an RDG from Aligned Consen
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Creating a Project Template 5 5 Thi
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Creating a Project Template Creatin
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Saving Project Components Saving Pr
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Creating and Analyzing a Project 6
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Workflow for This Chapter Before Yo
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Using the New Project Wizard to Cre
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Adding Specimens and Importing Data
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Analyzing the Data 5. Click OK. A n
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Reanalyzing a Project Using a Diffe
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Incorporating Variants into the Pro
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Viewing the Results 7 7 This chapte
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About the Project Data About the Pr
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Project Views Table 7-1 Project Vie
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Segment Views Segment Views There a
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Segment Views Table 7-2 Segment Vie
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Sample Views Sample Views The sampl
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Sample Views Table 7-4 Sample Views
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Sample Views Table 7-4 Sample Views
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Viewing Variants Method 2 1. Open t
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Viewing the Reports Viewing the Rep
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Viewing the Reports and Project Res
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Analysis QC Report Figure 7-3 Analy
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Mutations Report The Mutations repo
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AA Variants Report AA Variants Repo
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Sequence Confirmation Report Sequen
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Library Search Report Library Searc
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RDG Report RDG Report The report co
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Genotyping Report Genotyping Report
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Genotyping Report Figure 7-12 Genot
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Customizing the Reports 2. Select o
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Reanalyzing and Editing Data 8 8 Th
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About Analysis Parameters About Ana
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About Analysis Parameters Table 8-1
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Changing the Analysis Parameters in
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Editing the Data Editing the Data A
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Editing a Sample or a Consensus Seq
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Adjusting the Clear Range The three
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Adjusting the Clear Range Using the
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Editing Variants Method 2 To view a
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Exporting and Printing Data and Rep
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Exporting Data Files Exporting Data
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Exporting Data Files Exporting a Sp
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Exporting Data Files Exporting a Sa
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Exporting Reports Exporting a Repor
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Printing Data and Reports Printing
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Printing Data and Reports 3. Select
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Printing Data and Reports 4. Select
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Printing Data and Reports 6. Use th
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Printing Data and Reports Table 9-3
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Sample and Consensus Quality Values
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Sample Quality Values Sample Qualit
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Consensus Quality Values Consensus
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Displaying Quality Values Customizi
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Displaying Quality Values Displayin
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Cumulative Quality Value Scoring in
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Cumulative Quality Value Scoring in
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Automating Analysis 11 11 This chap
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Integrating SeqScape and Data Colle
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Before You Start Is SeqScape proper
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Launching Autoanalysis Manger Launc
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Creating Required Files in the Data
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Scheduling and Starting a Run 2. Cl
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Understanding the Autoanalysis Mana
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Understanding the Autoanalysis Mana
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Basecallers and DyeSet/Primer Files
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Definitions and Naming The DyeSet/P
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ABI PRISM SeqScape Software v2.1 Us
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Frequently Asked Questions B B This
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Training and Documentation FAQs Tra
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General SeqScape Software FAQs Gene
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General SeqScape Software FAQs Tabl
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SeqScape Manager FAQs SeqScape Mana
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SeqScape Manager FAQs Table B-5 Seq
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SeqScape Manager FAQs Table B-5 Seq
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Mutation, Variant, HIM, and HFM Det
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Data Analysis FAQs Table B-8 Data A
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Quality Values FAQs Table B-9 Analy
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Audit Trail, Security, and Access C
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Translation Tables C C This appendi
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IUPAC Diagrams IUPAC Diagrams IUPAC
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Amino Acid Abbreviations Amino Acid
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User Privileges D D Tables of User
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Tables of User Privileges Table D-2
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Aligned Variant and FASTA File Form
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FASTA File Format FASTA File Format
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FASTA File Format Table E-1 Accepte
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Creating a Multi-Aligned FASTA File
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Method 1: Create a Multi-Aligned FA
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Software Warranty G G Computer Conf
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Limited Product Warranty Warranty L
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Glossary ABI basecaller administrat
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DyeSet/Primer file export FASTA for
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Sample Manager sample quality value
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Index Numerics 310 Basecaller and D
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creating a library 4-20 an RDG, abo
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learning software, wizard 4-6 libra
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S sample bases, editing 8-14 data,
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Headquarters 850 Lincoln Centre Dri
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