SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications

Save this PDF as:
 WORD  PNG  TXT  JPG

Size: px
Start display at page:

Download "SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications"

Transcription

1 Product Bulletin Sequencing Software SeqScape Software Version 2.5 Comprehensive Analysis Solution for Resequencing Applications Comprehensive reference sequence handling Helps interpret the role of each polymorphism Accurate data analysis Detects heterozygous indels and provides quality values Two-tier analysis Reduces analysis time and complexity Powerful data visualization tools Allow you to focus on relevant data and create custom views of the same data Detailed reports Generates comprehensive reports with detailed results describing data quality Automation Integrated with Data Collection software to analyze raw data generated from Applied Biosystems genetic analyzers Introduction The goals of today s large resequencing studies are to detect SNPs, profile mutations, perform medical sequencing, identify haplotypes, subtype pathogens, and confirm clone constructs. For all of these applications, SeqScape software provides two levels of analysis SNP detection and the identification of sequences that most closely match a target sequence. Unlike tools initially designed for de novo analysis, SeqScape software is a comprehensive resequencing tool that analyzes data using full sequencefeature information, such as exon/ intron boundaries, translation frames, coding regions, and transcripts. No other software tool available manages gene complexity as well as SeqScape software, which provides accurate and reliable reports for all references, from the simplest to the most complex. Whether your research spans multiple genes or focuses on a single region of interest, SeqScape software supplies you with comprehensive referencesequence features, accurate polymorphism detection, powerful viewing features, and detailed reports that can be exported for use in other analyses. Flexibility to Configure a Reference The level of relevant information to be extracted from resequencing data depends not only on the quality of subject-sample sequences, but also on the reference sequence. The Reference Data Group (RDG), an advanced feature in SeqScape software, offers powerful capabilities for configuring reference sequence. For instance, you can directly import a GenBank SM file as a reference (Figure 1).

2 Figure 1. This figure shows a GenBank, format file downloaded from the NCBI public database. The sequence information from the GenBank file can be directly imported into the Reference Data Group (RDG) to use as a reference sequence. The software will automatically parse feature information from the file, including exon and intron boundaries, and translation information. This powerful feature allows the software to report mutations, nucleotides, or amino acids in the context of the genomic annotation. When studying a large gene, you can easily split the reference into smaller segments and delete any regions not required for a faster and easier data review. You can also configure alternate gene transcripts as layers, with different translation frames (Figure 2). You can even create a single template to use the same reference for multiple studies, and save time by avoiding repetitive steps. Complete Workflow The software lets you create a new project simply by selecting a previously configured project template and adding the subject sample sequences. A click on the Analysis button is all that is required to initiate automated basecalling, trimming, assembly, consensus alignment, and reference comparison (Figure 3). Figure 2. Complex references can be configured as shown in this example for the gene CDKN2A, with alternate transcripts. The RDG functionality in SeqScape software allows you to define unique layers with independent translation frames for each transcript. Analysis algorithms are designed and calibrated with Applied Biosystems instrument-specifications and reagent characteristics to provide accurate bases with quality values for each mutation. Distinctions between poor- and highquality data are clearly defined, as the KB Basecaller and SeqScape software algorithms filter out low-quality and anomalous data to provide a highquality assembly. Quality values allow you to review your data. Using software that provides a complete workflow eliminates working with multiple tools to get to your results.

3 Figure 3. SeqScape software workflow. for accurate detection of heterozygote calls (Figure 5). This ensures accurate detection of all types of mutations, including heterozygous insertion or deletion mutations (HIMs), which are often missed by other methods. First-tier Analysis Detects Mutations with Confidence The first-tier analysis detects all variations between the reference sequence and the subject sample sequence, including deletions, insertions, mismatches, heterozygous bases, and heterozygous insertion/deletions. The consensus caller in SeqScape software examines the quality of each trace for background noise as well as the orientation of the traces, and forms an accurate consensus call. Variations between the consensus and the reference sequence are reported as mutations in the Mutations report. Analysis at the consensus level corrects sequencing anomalies such as PCR noise or unincorporated dye terminators that are present in one strand and cause a basecalling error (Figure 4). Algorithms at the consensus level are essential to reduce the false-positive rate Second-tier Analysis Identifies Best Sequence Matches from an Allele Library Second-tier analysis compares each consensus sequence to a library of sequences and identifies the best matches, an important step in identification studies. Most labs must invest in additional software to perform this level of analysis. SeqScape software allows you to compare your sample data with a library of allelic sequences and perform a haploid or diploid search to identify the best matches. Results of alignment and identification are reported within the Library Search report (Figure 6). Figure 4. This figures shows an example of an accurate consensus generated using base quality information from the forward and reverse strands. The consensus calling algorithm corrects for miscalls in individual strands (indicated by red dots). Figure 5. A heterozygous deletion mutation is correctly identified and reported by SeqScape software algorithms.

4 Powerful Data Visualization Tools Sophisticated data visualization tools enable you to navigate effortlessly through large data sets and screen out non-relevant data. Thus, you can scan thousands of data points quickly and easily for mutations (Figure 7). The software allows you to view an assembly of the entire project or of each individual specimen (Figure 8). Detailed Reports Results reports from SeqScape software include hyperlinks to the data source to show the relationship between the results and the data (Figure 9). For each mutation detected, you can review the quality value provided, the classification of novel or known SNP, and the impact of the SNP on the amino acid translation level. Mutations can be sorted by each of these attributes for easy and fast review. You can also view the audit history of changes made to base pairs in the Audit report. Figure 6. For library searching, a library of pre-aligned sequences is imported into the Library Editor and aligned with the Reference Data Group (RDG). After analysis is complete, the results are reported in the Library Search report. Export Capabilities for Easy Integration SeqScape software provides a complete analysis, which usually requires several analysis tools. It also enables researchers to easily import results into other software packages or archival mechanisms. SeqScape software stores results in detailed reports and enables flexible exporting options. A variety of export functionalities are provided, including alignment of the complete project, assembly across a reference segment, and individual consensus, in standard FASTA format. You can export the reports in convenient formats, such as tab-delimited text, html, and xml for easy integration into downstream pipelines. Figure 7. In the Character/Dots view, base differences in the consensus are displayed against the reference as characters, and all bases common to the reference are represented as dots.

5 Security Features Requires user ID and password to enter the software Displays name when user is logged into the system Provides unique user ID and password for each user Figure 8. Specimen view illustrates the assembly of individual traces (forward and reverse) across the complete reference. Specifies password lifetime Prevents unauthorized user ID or password Audit Trail Features Generates an audit trail when bases are changed, added, or deleted Contains user name, time and date of each change, and the reason for each change Figure 9. Base changes reported in the Mutations Report can be directly linked to view the sample data. Automation Features Increase Productivity SeqScape software is the only mutation analysis software fully integrated with Applied Biosystems Data Collection software and reagents, which are designed expressly for our DNA sequencing instruments. SeqScape Software v2.5, together with Data Collection Software v3.0, automates data analysis, so you can concentrate on data review. By creating a SeqScape Software plate in Data Collection software, you can run an automated analysis pipeline that will generate project analysis reports in SeqScape software. Assists with 21 CFR Part 11 Requirements For researchers working in regulated environments, SeqScape software offers a full suite of features to provide data security, an audit trail of data changes, and electronic signatures. These features, which are designed to assist customers with 21CFR part 11 requirements and can be disabled or enabled at the time of software installation, include the following: Electronic Signatures Captures the printed name of the signer, the date and time of the signature, and the meaning associated with the signature Provides a unique electronic signature for each user Free 45-day Download and Webinars SeqScape Software v2.5 is available (/support/ software) as a 45-day free demo for use with your own data. For more information, contact your Applied Biosystems sales representative. Free Webinars are also available to provide introductory training on the software. For a schedule of upcoming Webinars, visit: info.appliedbiosystems.com/ webinars.

6 Ordering Information Description P/N SeqScape Software v2.5, Initial License SeqScape Software v2.5, 45-Day Demo and Tutorial,** 1 pack/5 users SeqScape Software v2.5 and DNA Sequencing Analysis Software v5.2, Initial License ABI PRISM 310 Genetic Analyzer Sequencing Analysis Software v5.2 and SeqScape Software v2.5, Initial License Sequencing Analysis Software v5.2, SeqScape Software v2.5, & GeneMapper SW v4.0, 1 license Applied Biosystems 3130/3130xl Genetic Analyzer Sequencing Analysis Software v5.2 and SeqScape Software v2.5, Initial License Sequencing Analysis v5.2, SeqScape v2.5, & GeneMapper Software v4.0, 1 license Upgrades from the 3100 Avant to the 3130/3130xl Genetic Analyzer Sequencing Analysis Software v5.2 and SeqScape Software v2.5, 1 license Applied Biosystems 3730/3730xl Genetic Analyzer Sequencing Analysis v5.2 and SeqScape Software v2.5, 3 licenses Sequencing Analysis v5.2, SeqScape v2.5, & GeneMapper Software v4.0, 3 licenses Additional License* SeqScape Software v Upgrades/Updates Upgrade to SeqScape Software v2.5 from v1.0/ Update to SeqScape Software v2.5 from v2.0/2.1.1** **User has an initial license. **Free download from For Research Use Only. Not for use in diagnostic procedures. 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 Applera Corporation, either expressly, or by estoppel. SeqScape Software has not undergone specific developmental validation for human identification applications. Human identification laboratories that choose to use SeqScape Software for data analysis should perform their own developmental validation studies. ABI PRISM, Applied Biosystems, GeneMapper, and SeqScape are registered trademarks and AB (Design), Applera, and KB are trademarks of the Applera Corporation or its subsidiaries in the US and/or certain other countries. GenBank is a service mark of the US Department of Health and Human Services. Macintosh is a registered trademark of Apple Computer. Windows is a registered trademark of Microsoft Corporation. All other trademarks are the sole property of their respective owners Applied Biosystems. All Rights Reserved. Printed in the USA, 06/2005, LD Publication 133PB02-01 Headquarters 850 Lincoln Centre Drive Foster City, CA USA Phone Toll Free International Sales For our office locations, please call the division headquarters or refer to our Web site at /about/offices.cfm

SUBJECT: New Features in Version 5.3

SUBJECT: New Features in Version 5.3 User Bulletin Sequencing Analysis Software v5.3 July 2007 SUBJECT: New Features in Version 5.3 This user bulletin includes the following topics: New Features in v5.3.....................................

More information

AS4.1 190509 Replaces 260806 Page 1 of 50 ATF. Software for. DNA Sequencing. Operators Manual. Assign-ATF is intended for Research Use Only (RUO):

AS4.1 190509 Replaces 260806 Page 1 of 50 ATF. Software for. DNA Sequencing. Operators Manual. Assign-ATF is intended for Research Use Only (RUO): Replaces 260806 Page 1 of 50 ATF Software for DNA Sequencing Operators Manual Replaces 260806 Page 2 of 50 1 About ATF...5 1.1 Compatibility...5 1.1.1 Computer Operator Systems...5 1.1.2 DNA Sequencing

More information

User Bulletin. GeneMapper Software Version 4.0. Installation Options. In This User Bulletin. Overview

User Bulletin. GeneMapper Software Version 4.0. Installation Options. In This User Bulletin. Overview User Bulletin Software Version 4.0 February 2006 SUBJECT: Installation Options In This User Bulletin Overview This user bulletin covers:............................... 2 Installation Options for the........

More information

SNPbrowser Software v3.5

SNPbrowser Software v3.5 Product Bulletin SNP Genotyping SNPbrowser Software v3.5 A Free Software Tool for the Knowledge-Driven Selection of SNP Genotyping Assays Easily visualize SNPs integrated with a physical map, linkage disequilibrium

More information

Sequencing Analysis Software Version 5.1

Sequencing Analysis Software Version 5.1 Applied Biosystems DNA Sequencing Analysis Software Sequencing Analysis Software Version 5.1 The Applied Biosystems DNA Sequencing Analysis Software v5.1 is designed to analyze, display, edit, save, and

More information

Replacing TaqMan SNP Genotyping Assays that Fail Applied Biosystems Manufacturing Quality Control. Begin

Replacing TaqMan SNP Genotyping Assays that Fail Applied Biosystems Manufacturing Quality Control. Begin User Bulletin TaqMan SNP Genotyping Assays May 2008 SUBJECT: Replacing TaqMan SNP Genotyping Assays that Fail Applied Biosystems Manufacturing Quality Control In This Bulletin Overview This user bulletin

More information

Sequencing Analysis Software Version 5.4

Sequencing Analysis Software Version 5.4 Applied Biosystems Sequencing Analysis Software Quick Reference Card Sequencing Analysis Software Version 5.4 Applied Biosystems Sequencing Analysis Software v5.4 analyzes, displays, edits, saves, and

More information

Quantifiler Human DNA Quantification Kit Quantifiler Y Human Male DNA Quantification Kit

Quantifiler Human DNA Quantification Kit Quantifiler Y Human Male DNA Quantification Kit Product Bulletin Human Identification Quantifiler Human DNA Quantification Kit Quantifiler Y Human Male DNA Quantification Kit The Quantifiler kits produce reliable and reproducible results, helping to

More information

RETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison

RETRIEVING SEQUENCE INFORMATION. Nucleotide sequence databases. Database search. Sequence alignment and comparison RETRIEVING SEQUENCE INFORMATION Nucleotide sequence databases Database search Sequence alignment and comparison Biological sequence databases Originally just a storage place for sequences. Currently the

More information

ABI PRISM 310 Genetic Analyzer

ABI PRISM 310 Genetic Analyzer ABI PRISM 310 Genetic Analyzer Upgrading Data Collection Software to the Windows Platform Software Installation Guide May 12, 2004 4:24 pm, Title.fm Copyright 2004 Applied Biosystems. All rights reserved.

More information

Focusing on results not data comprehensive data analysis for targeted next generation sequencing

Focusing on results not data comprehensive data analysis for targeted next generation sequencing Focusing on results not data comprehensive data analysis for targeted next generation sequencing Daniel Swan, Jolyon Holdstock, Angela Matchan, Richard Stark, John Shovelton, Duarte Mohla and Simon Hughes

More information

A Fast, Accurate, and Automated Workflow for Multi Locus Sequence Typing of Bacterial Isolates

A Fast, Accurate, and Automated Workflow for Multi Locus Sequence Typing of Bacterial Isolates Application Note MLST A Fast, Accurate, and Automated Workflow for Multi Locus Sequence Typing of Bacterial Isolates Using Applied Biosystems 3130 and 3730 Series Capillary Electrophoresis Systems and

More information

Software Getting Started Guide

Software Getting Started Guide Software Getting Started Guide For Research Use Only. Not for use in diagnostic procedures. P/N 001-097-569-03 Copyright 2010-2013, Pacific Biosciences of California, Inc. All rights reserved. Information

More information

User Guide for the 21 CFR Part 11 Module in SDS Software v1.4

User Guide for the 21 CFR Part 11 Module in SDS Software v1.4 Applied Biosystems 7500/7500 Fast Real-Time PCR System User Guide for the 21 CFR Part 11 Module in SDS Software v1.4 Introduction Installation Logging in to the SDS Software Configuring the 21CFR11 Module

More information

LifeScope Genomic Analysis Software 2.5

LifeScope Genomic Analysis Software 2.5 USER GUIDE LifeScope Genomic Analysis Software 2.5 Graphical User Interface DATA ANALYSIS METHODS AND INTERPRETATION Publication Part Number 4471877 Rev. A Revision Date November 2011 For Research Use

More information

GeneMapper ID-X Software Version 1.0

GeneMapper ID-X Software Version 1.0 Administrator s Guide GeneMapper ID-X Software Version 1.0 Note: To improve the clarity of graphics in this PDF file, use the zoom tool to increase magnification to 150% or greater. Administrator s Guide

More information

Tour Guide for Windows and Macintosh

Tour Guide for Windows and Macintosh Tour Guide for Windows and Macintosh 2007 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Suite 100A, Ann Arbor, MI 48108 USA phone 1.800.497.4939 or 1.734.769.7249 (fax) 1.734.769.7074

More information

The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics

The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics The Power of Next-Generation Sequencing in Your Hands On the Path towards Diagnostics The GS Junior System The Power of Next-Generation Sequencing on Your Benchtop Proven technology: Uses the same long

More information

Applied Biosystems 7500/7500 Fast Real-Time PCR Systems. SUBJECT: Memory Upgrade Requirements for 7500 Software v2.0

Applied Biosystems 7500/7500 Fast Real-Time PCR Systems. SUBJECT: Memory Upgrade Requirements for 7500 Software v2.0 User Bulletin Applied Biosystems 7500/7500 Fast Real-Time PCR Systems February 2008 SUBJECT: Memory Upgrade Requirements for 7500 Software v2.0 In This User Bulletin Summary This user bulletin covers:

More information

User Bulletin. 8200 Cellular Detection System Analysis Software v4.0. Introduction. 21 CFR Part 11 Software Console - Administrators Guide

User Bulletin. 8200 Cellular Detection System Analysis Software v4.0. Introduction. 21 CFR Part 11 Software Console - Administrators Guide . User Bulletin 8200 Cellular Detection System Analysis Software v4.0 August 14, 2007 SUBJECT: 21 CFR Part 11 Software Console - Administrators Guide In This User Bulletin This user bulletin covers: Introduction.......................................................

More information

Bioinformatics Resources at a Glance

Bioinformatics Resources at a Glance Bioinformatics Resources at a Glance A Note about FASTA Format There are MANY free bioinformatics tools available online. Bioinformaticists have developed a standard format for nucleotide and protein sequences

More information

Security, Audit, and e-signature Administrator Console v1.2.x

Security, Audit, and e-signature Administrator Console v1.2.x Security, Audit, and e-signature Administrator Console v1.2.x USER GUIDE SAE Admin Console for use with: QuantStudio Design and Analysis desktop Software Publication Number MAN0010410 Revision A.0 For

More information

Getting Started Guide

Getting Started Guide Primer Express Software Version 3.0 Getting Started Guide Before You Begin Designing Primers and Probes for Quantification Assays Designing Primers and Probes for Allelic Discrimination Assays Ordering

More information

CUSTOM DNA SEQUENCING SERVICES

CUSTOM DNA SEQUENCING SERVICES CUSTOM DNA SEQUENCING SERVICES Satisfied Customers are our Driving Force We never stop exceeding your Expectations Value Read Service Single read sequencing of plasmid inserts or PCR products in tube and

More information

Custom TaqMan Assays For New SNP Genotyping and Gene Expression Assays. Design and Ordering Guide

Custom TaqMan Assays For New SNP Genotyping and Gene Expression Assays. Design and Ordering Guide Custom TaqMan Assays For New SNP Genotyping and Gene Expression Assays Design and Ordering Guide For Research Use Only. Not intended for any animal or human therapeutic or diagnostic use. Information in

More information

Installation and Administration Guide

Installation and Administration Guide GeneMapper Software Version 4.0 Installation and Administration Guide Getting Started Installation Requirements and Software Compatibility Performing a New Installation of the GeneMapper Software Upgrading

More information

Delivering the power of the world s most successful genomics platform

Delivering the power of the world s most successful genomics platform Delivering the power of the world s most successful genomics platform NextCODE Health is bringing the full power of the world s largest and most successful genomics platform to everyday clinical care NextCODE

More information

Sequence Analysis Instructions

Sequence Analysis Instructions Sequence Analysis Instructions In order to predict your drug metabolizing phenotype from your CYP2D6 gene sequence, you must determine: 1) The assembled sequence from your two opposing sequencing reactions

More information

Tutorial for Windows and Macintosh. Preparing Your Data for NGS Alignment

Tutorial for Windows and Macintosh. Preparing Your Data for NGS Alignment Tutorial for Windows and Macintosh Preparing Your Data for NGS Alignment 2015 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) 1.734.769.7249

More information

GenBank, Entrez, & FASTA

GenBank, Entrez, & FASTA GenBank, Entrez, & FASTA Nucleotide Sequence Databases First generation GenBank is a representative example started as sort of a museum to preserve knowledge of a sequence from first discovery great repositories,

More information

Simplifying Data Interpretation with Nexus Copy Number

Simplifying Data Interpretation with Nexus Copy Number Simplifying Data Interpretation with Nexus Copy Number A WHITE PAPER FROM BIODISCOVERY, INC. Rapid technological advancements, such as high-density acgh and SNP arrays as well as next-generation sequencing

More information

Version 5.0 Release Notes

Version 5.0 Release Notes Version 5.0 Release Notes 2011 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) +1.734.769.7249 (elsewhere) +1.734.769.7074 (fax) www.genecodes.com

More information

TaqMan Genotyper Software v1.0.1 TaqMan Genotyping Data Analysis Software

TaqMan Genotyper Software v1.0.1 TaqMan Genotyping Data Analysis Software TaqMan Genotyper Software v1.0.1 TaqMan Genotyping Data Analysis Software March 2011 Product Overview TaqMan Genotyper Software TaqMan Genotyper Software Standalone data analysis software for Applied Biosystems

More information

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources

Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources 1 of 8 11/7/2004 11:00 AM National Center for Biotechnology Information About NCBI NCBI at a Glance A Science Primer Human Genome Resources Model Organisms Guide Outreach and Education Databases and Tools

More information

Genomes and SNPs in Malaria and Sickle Cell Anemia

Genomes and SNPs in Malaria and Sickle Cell Anemia Genomes and SNPs in Malaria and Sickle Cell Anemia Introduction to Genome Browsing with Ensembl Ensembl The vast amount of information in biological databases today demands a way of organising and accessing

More information

When you install Mascot, it includes a copy of the Swiss-Prot protein database. However, it is almost certain that you and your colleagues will want

When you install Mascot, it includes a copy of the Swiss-Prot protein database. However, it is almost certain that you and your colleagues will want 1 When you install Mascot, it includes a copy of the Swiss-Prot protein database. However, it is almost certain that you and your colleagues will want to search other databases as well. There are very

More information

Next Generation Sequencing: Technology, Mapping, and Analysis

Next Generation Sequencing: Technology, Mapping, and Analysis Next Generation Sequencing: Technology, Mapping, and Analysis Gary Benson Computer Science, Biology, Bioinformatics Boston University gbenson@bu.edu http://tandem.bu.edu/ The Human Genome Project took

More information

Single Nucleotide Polymorphism (SNP) Calling from Next-Gen Sequencing (NGS) data for Bacterial Phylogenetics

Single Nucleotide Polymorphism (SNP) Calling from Next-Gen Sequencing (NGS) data for Bacterial Phylogenetics Single Nucleotide Polymorphism (SNP) Calling from Next-Gen Sequencing (NGS) data for Bacterial Phylogenetics Taj Azarian, MPH Doctoral Student Department of Epidemiology College of Medicine and College

More information

Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University

Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University Amira A. AL-Hosary PhD of infectious diseases Department of Animal Medicine (Infectious Diseases) Faculty of Veterinary Medicine Assiut University Egypt Interpretation of sequence results An overview on

More information

SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis

SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis SeattleSNPs Interactive Tutorial: Web Tools for Site Selection, Linkage Disequilibrium and Haplotype Analysis Goal: This tutorial introduces several websites and tools useful for determining linkage disequilibrium

More information

The Financial Benefits of the MicroSEQ Microbial Identification System

The Financial Benefits of the MicroSEQ Microbial Identification System White paper Financial Benefits of the MicroSEQ Microbial Identification System The Financial Benefits of the MicroSEQ Microbial Identification System Up to 160% ROI over 3 years, Break-even as soon as

More information

4.2.1. What is a contig? 4.2.2. What are the contig assembly programs?

4.2.1. What is a contig? 4.2.2. What are the contig assembly programs? Table of Contents 4.1. DNA Sequencing 4.1.1. Trace Viewer in GCG SeqLab Table. Box. Select the editor mode in the SeqLab main window. Import sequencer trace files from the File menu. Select the trace files

More information

Introduction to Bioinformatics 3. DNA editing and contig assembly

Introduction to Bioinformatics 3. DNA editing and contig assembly Introduction to Bioinformatics 3. DNA editing and contig assembly Benjamin F. Matthews United States Department of Agriculture Soybean Genomics and Improvement Laboratory Beltsville, MD 20708 matthewb@ba.ars.usda.gov

More information

Tutorial for Windows and Macintosh Quality Scores

Tutorial for Windows and Macintosh Quality Scores Tutorial for Windows and Macintosh Quality Scores 2016 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) +1.734.769.7249 (elsewhere) +1.734.769.7074

More information

Biological Sequence Data Formats

Biological Sequence Data Formats Biological Sequence Data Formats Here we present three standard formats in which biological sequence data (DNA, RNA and protein) can be stored and presented. Raw Sequence: Data without description. FASTA

More information

Artisan Scientific is You~ Source for: Quality New and Certified-Used/Pre:-awned ECJuiflment

Artisan Scientific is You~ Source for: Quality New and Certified-Used/Pre:-awned ECJuiflment Looking for more information? Visit us on the web at http://www.artisan-scientific.com for more information: Price Quotations Drivers Technical Specifications. Manuals and Documentation Artisan Scientific

More information

DNA Sequence Analysis Tutorial Genetics Laboratory

DNA Sequence Analysis Tutorial Genetics Laboratory DNA Sequence Analysis Tutorial Genetics Laboratory By Jason Evans, Luke Sheneman and Celeste Brown 1 What is VectorNTI? From the Informax website: VectorNTI equips laboratories with an extensive range

More information

Data Analysis on the ABI PRISM 7700 Sequence Detection System: Setting Baselines and Thresholds. Overview. Data Analysis Tutorial

Data Analysis on the ABI PRISM 7700 Sequence Detection System: Setting Baselines and Thresholds. Overview. Data Analysis Tutorial Data Analysis on the ABI PRISM 7700 Sequence Detection System: Setting Baselines and Thresholds Overview In order for accuracy and precision to be optimal, the assay must be properly evaluated and a few

More information

Vector NTI Advance 11.5 Quick Start Guide Catalog no , ,

Vector NTI Advance 11.5 Quick Start Guide Catalog no , , Vector NTI Advance 11.5 Quick Start Guide Catalog no. 12605050, 12605099, 12605103 Part no. 12605-022 Revision date: 10 October 2010 MAN0000419 User Manual 2010 Life Technologies Corporation. All rights

More information

Generating ABI PRISM 7700 Standard Curve Plots in a Spreadsheet Program

Generating ABI PRISM 7700 Standard Curve Plots in a Spreadsheet Program Generating ABI PRISM 7700 Standard Curve Plots in a Spreadsheet Program Overview The goal of this tutorial is to demonstrate the procedure through which analyzed data generated within an ABI PRISM 7700

More information

Analysis of NGS Data

Analysis of NGS Data Analysis of NGS Data Introduction and Basics Folie: 1 Overview of Analysis Workflow Images Basecalling Sequences denovo - Sequencing Assembly Annotation Resequencing Alignments Comparison to reference

More information

Exercise 11 - Understanding the Output for a blastn Search (excerpted from a document created by Wilson Leung, Washington University)

Exercise 11 - Understanding the Output for a blastn Search (excerpted from a document created by Wilson Leung, Washington University) Exercise 11 - Understanding the Output for a blastn Search (excerpted from a document created by Wilson Leung, Washington University) Read the following tutorial to better understand the BLAST report for

More information

New Features in Primavera P6 EPPM 15.2

New Features in Primavera P6 EPPM 15.2 New Features in Primavera P6 EPPM 15.2 COPYRIGHT & TRADEMARKS Copyright 2015, Oracle and/or its affiliates. All rights reserved. Oracle is a registered trademark of Oracle Corporation and/or its affiliates.

More information

NSilico Life Science Introductory Bioinformatics Course

NSilico Life Science Introductory Bioinformatics Course NSilico Life Science Introductory Bioinformatics Course INTRODUCTORY BIOINFORMATICS COURSE A public course delivered over three days on the fundamentals of bioinformatics and illustrated with lectures,

More information

Single-Cell Whole Genome Sequencing on the C1 System: a Performance Evaluation

Single-Cell Whole Genome Sequencing on the C1 System: a Performance Evaluation PN 100-9879 A1 TECHNICAL NOTE Single-Cell Whole Genome Sequencing on the C1 System: a Performance Evaluation Introduction Cancer is a dynamic evolutionary process of which intratumor genetic and phenotypic

More information

Table of Contents. DiversiTree Tutorial! 1 of 29

Table of Contents. DiversiTree Tutorial! 1 of 29 DiversiTree Tutorial! 1 of 29 Table of Contents Part 1: The DiversiTree Application Overview... 2 Search Pane & Search Categories... 3 Result & Data Windows... 4 Trace Archives... 5 User Created Lists...

More information

Clone Manager. Getting Started

Clone Manager. Getting Started Clone Manager for Windows Professional Edition Volume 2 Alignment, Primer Operations Version 9.5 Getting Started Copyright 1994-2015 Scientific & Educational Software. All rights reserved. The software

More information

Introduction to NGS data analysis

Introduction to NGS data analysis Introduction to NGS data analysis Jeroen F. J. Laros Leiden Genome Technology Center Department of Human Genetics Center for Human and Clinical Genetics Sequencing Illumina platforms Characteristics: High

More information

Guideline for the submission of DNA sequences and associated annotations within the framework of Directive 2001/18/EC and Regulation (EC) No 1829/2003

Guideline for the submission of DNA sequences and associated annotations within the framework of Directive 2001/18/EC and Regulation (EC) No 1829/2003 Guideline for the submission of DNA sequences and associated annotations within the framework of Directive 2001/18/EC and Regulation (EC) No 1829/2003 European Reference Laboratory for Genetically Modified

More information

Single Nucleotide Polymorphisms (SNPs)

Single Nucleotide Polymorphisms (SNPs) Single Nucleotide Polymorphisms (SNPs) Additional Markers 13 core STR loci Obtain further information from additional markers: Y STRs Separating male samples Mitochondrial DNA Working with extremely degraded

More information

The GeneAmp PCR System 9700. Results you can trust. A PCR platform you can grow with. GeneAmp. PCR System 9700

The GeneAmp PCR System 9700. Results you can trust. A PCR platform you can grow with. GeneAmp. PCR System 9700 The GeneAmp PCR System 9700 Results you can trust. A PCR platform you can grow with. GeneAmp PCR System 9700 The GeneAmp PCR System 9700 fits your lab bench, your applications and your budget. The GeneAmp

More information

Go where the biology takes you. Genome Analyzer IIx Genome Analyzer IIe

Go where the biology takes you. Genome Analyzer IIx Genome Analyzer IIe Go where the biology takes you. Genome Analyzer IIx Genome Analyzer IIe Go where the biology takes you. To published results faster With proven scalability To the forefront of discovery To limitless applications

More information

Microsoft Dynamics GP. Electronic Signatures

Microsoft Dynamics GP. Electronic Signatures Microsoft Dynamics GP Electronic Signatures Copyright Copyright 2006 Microsoft Corporation. All rights reserved. Complying with all applicable copyright laws is the responsibility of the user. Without

More information

Geospiza s Finch-Server: A Complete Data Management System for DNA Sequencing

Geospiza s Finch-Server: A Complete Data Management System for DNA Sequencing KOO10 5/31/04 12:17 PM Page 131 10 Geospiza s Finch-Server: A Complete Data Management System for DNA Sequencing Sandra Porter, Joe Slagel, and Todd Smith Geospiza, Inc., Seattle, WA Introduction The increased

More information

Xcalibur. Foundation. Administrator Guide. Software Version 3.0

Xcalibur. Foundation. Administrator Guide. Software Version 3.0 Xcalibur Foundation Administrator Guide Software Version 3.0 XCALI-97520 Revision A May 2013 2013 Thermo Fisher Scientific Inc. All rights reserved. LCquan, Watson LIMS, and Web Access are trademarks,

More information

CAP BIOINFORMATICS Su-Shing Chen CISE. 10/5/2005 Su-Shing Chen, CISE 1

CAP BIOINFORMATICS Su-Shing Chen CISE. 10/5/2005 Su-Shing Chen, CISE 1 CAP 5510-8 BIOINFORMATICS Su-Shing Chen CISE 10/5/2005 Su-Shing Chen, CISE 1 Genomic Mapping & Mapping Databases High resolution, genome-wide maps of DNA markers. Integrated maps, genome catalogs and comprehensive

More information

MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification

MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification MultiQuant Software 2.0 for Targeted Protein / Peptide Quantification Gold Standard for Quantitative Data Processing Because of the sensitivity, selectivity, speed and throughput at which MRM assays can

More information

Protocol. Introduction to TaqMan and SYBR Green Chemistries for Real-Time PCR

Protocol. Introduction to TaqMan and SYBR Green Chemistries for Real-Time PCR Protocol Introduction to TaqMan and SYBR Green Chemistries for Real-Time PCR Copyright 2008, 2010 Applied Biosystems. All rights reserved. Ambion and Applied Biosystems products are for Research Use Only.

More information

AuthentiMax Software for GloMax -Multi+

AuthentiMax Software for GloMax -Multi+ TECHNICAL MANUAL AuthentiMax Software for GloMax -Multi+ Instruc ons for use of Product E8946. TM403 Revised 9/13 AuthentiMax Software for GloMax -Multi+ All technical literature is available on the Internet

More information

Data Analysis for Ion Torrent Sequencing

Data Analysis for Ion Torrent Sequencing IFU022 v140202 Research Use Only Instructions For Use Part III Data Analysis for Ion Torrent Sequencing MANUFACTURER: Multiplicom N.V. Galileilaan 18 2845 Niel Belgium Revision date: August 21, 2014 Page

More information

Searching Nucleotide Databases

Searching Nucleotide Databases Searching Nucleotide Databases 1 When we search a nucleic acid databases, Mascot always performs a 6 frame translation on the fly. That is, 3 reading frames from the forward strand and 3 reading frames

More information

ONE WORKFLOW. ONE PARTNER. ACTIONABLE INSIGHTS. Sample to Insight

ONE WORKFLOW. ONE PARTNER. ACTIONABLE INSIGHTS. Sample to Insight ONE WORKFLOW. ONE PARTNER. ACTIONABLE INSIGHTS. Sample to Insight (NGS) Nucleic Acid More actionable data and insights in one go. More confidence at one glance. A small step for you, a giant leap for your

More information

LESSON 9. Analyzing DNA Sequences and DNA Barcoding. Introduction. Learning Objectives

LESSON 9. Analyzing DNA Sequences and DNA Barcoding. Introduction. Learning Objectives 9 Analyzing DNA Sequences and DNA Barcoding Introduction DNA sequencing is performed by scientists in many different fields of biology. Many bioinformatics programs are used during the process of analyzing

More information

Supervised DNA barcodes species classification: analysis, comparisons and results. Tutorial. Citations

Supervised DNA barcodes species classification: analysis, comparisons and results. Tutorial. Citations Supervised DNA barcodes species classification: analysis, comparisons and results Emanuel Weitschek, Giulia Fiscon, and Giovanni Felici Citations If you use this procedure please cite: Weitschek E, Fiscon

More information

SOLUTIONS FOR NEXT-GENERATION SEQUENCING

SOLUTIONS FOR NEXT-GENERATION SEQUENCING SOLUTIONS FOR NEXT-GENERATION SEQUENCING GENOMICS CELL BIOLOGY PROTEOMICS AUTOMATION enabling next-generation research From Samples To Publication, Millennium Science Enables Your Next-Gen Sequencing Workflow

More information

Applied Biosystems Genetic Analyzers Gold-standard technologies for Sanger sequencing and fragment analysis applications

Applied Biosystems Genetic Analyzers Gold-standard technologies for Sanger sequencing and fragment analysis applications Applied Biosystems Genetic Analyzers Gold-standard technologies for Sanger sequencing and fragment analysis applications Sequence with confidence Today, DNA sequencing is a fundamental tool in basic, applied

More information

Surveyor. DNA Variant Analysis Software. Mutation. SoftGenetics LLC. v 3.1. 200 Innovation Blvd, Suite 235 State College PA 16803 USA 814/237/9340

Surveyor. DNA Variant Analysis Software. Mutation. SoftGenetics LLC. v 3.1. 200 Innovation Blvd, Suite 235 State College PA 16803 USA 814/237/9340 Mutation Surveyor DNA Variant Analysis Software v 3.1 SoftGenetics LLC 200 Innovation Blvd, Suite 235 State College PA 16803 USA 814/237/9340 email: info@softgenetics.com technical service: tech_support@softgenetics.com

More information

Mitochondrial DNA Typing

Mitochondrial DNA Typing Tutorial for Windows and Macintosh Mitochondrial DNA Typing 2010 Gene Codes Corporation Gene Codes Corporation 775 Technology Drive, Ann Arbor, MI 48108 USA 1.800.497.4939 (USA) +1.734.769.7249 (elsewhere)

More information

Real-time qpcr Assay Design Software www.qpcrdesign.com

Real-time qpcr Assay Design Software www.qpcrdesign.com Real-time qpcr Assay Design Software www.qpcrdesign.com Your Blueprint For Success Informational Guide 2199 South McDowell Blvd Petaluma, CA 94954-6904 USA 1.800.GENOME.1(436.6631) 1.415.883.8400 1.415.883.8488

More information

Using Illumina BaseSpace Apps to Analyze RNA Sequencing Data

Using Illumina BaseSpace Apps to Analyze RNA Sequencing Data Using Illumina BaseSpace Apps to Analyze RNA Sequencing Data The Illumina TopHat Alignment and Cufflinks Assembly and Differential Expression apps make RNA data analysis accessible to any user, regardless

More information

EventTracker: Configuring DLA Extension for AWStats report AWStats Reports

EventTracker: Configuring DLA Extension for AWStats report AWStats Reports EventTracker: Configuring DLA Extension for AWStats report AWStats Reports Prism Microsystems Corporate Headquarter Date: October 18, 2011 8815 Centre Park Drive Columbia MD 21045 (+1) 410.953.6776 (+1)

More information

Monitoring SharePoint 2007/2010/2013 Server Using Event Tracker

Monitoring SharePoint 2007/2010/2013 Server Using Event Tracker Monitoring SharePoint 2007/2010/2013 Server Using Event Tracker White Paper Publication Date: June 2012 EventTracker 8815 Centre Park Drive Columbia MD 21045 www.eventtracker.com Overview EventTracker

More information

Chironomid DNA Barcode Database Search System. User Manual

Chironomid DNA Barcode Database Search System. User Manual Chironomid DNA Barcode Database Search System User Manual National Institute for Environmental Studies Center for Environmental Biology and Ecosystem Studies December 2015 Contents 1. Overview 1 2. Search

More information

EZValidation Online Tool. The easy way to apply guidelines. The EZValidation Online Tool. The implementation of new tests

EZValidation Online Tool. The easy way to apply guidelines. The EZValidation Online Tool. The implementation of new tests The implementation of new tests The EZValidation Online Tool Since 999, AcroMetrix has provided quality control requires validation or verification studies that meet is a comprehensive tool specifically

More information

SMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v2.2.0. 1.1 SMRT Analysis v2.2.0 Overview. Notes:

SMRT Analysis v2.2.0 Overview. 1. SMRT Analysis v2.2.0. 1.1 SMRT Analysis v2.2.0 Overview. Notes: SMRT Analysis v2.2.0 Overview 100 338 400 01 1. SMRT Analysis v2.2.0 1.1 SMRT Analysis v2.2.0 Overview Welcome to Pacific Biosciences' SMRT Analysis v2.2.0 Overview 1.2 Contents This module will introduce

More information

Visualization with the Integrative Genomics Viewer (IGV)

Visualization with the Integrative Genomics Viewer (IGV) Ecole de Bioinformatique Aviesan - Integrative Genomics Viewer (IGV) 1 Visualization with the Integrative Genomics Viewer (IGV) Elodie Girard Institut Curie U900 Inserm Mines ParisTech Ecole de Bioinformatique

More information

A complete workflow for pharmacogenomics using the QuantStudio 12K Flex Real-Time

A complete workflow for pharmacogenomics using the QuantStudio 12K Flex Real-Time Application NOte QuantStudio 12K Flex Real-Time PCR System A complete workflow for pharmacogenomics using the QuantStudio 12K Flex Real-Time PCR System Introduction Pharmacogenomics (PGx) is the study

More information

ORACLE USER PRODUCTIVITY KIT USAGE TRACKING ADMINISTRATION & REPORTING RELEASE 3.6 PART NO. E17087-01

ORACLE USER PRODUCTIVITY KIT USAGE TRACKING ADMINISTRATION & REPORTING RELEASE 3.6 PART NO. E17087-01 ORACLE USER PRODUCTIVITY KIT USAGE TRACKING ADMINISTRATION & REPORTING RELEASE 3.6 PART NO. E17087-01 FEBRUARY 2010 COPYRIGHT Copyright 1998, 2009, Oracle and/or its affiliates. All rights reserved. Part

More information

A Primer of Genome Science THIRD

A Primer of Genome Science THIRD A Primer of Genome Science THIRD EDITION GREG GIBSON-SPENCER V. MUSE North Carolina State University Sinauer Associates, Inc. Publishers Sunderland, Massachusetts USA Contents Preface xi 1 Genome Projects:

More information

Manual for Demo Data

Manual for Demo Data Manual for Demo Data SEQUENCE Pilot module SeqPatient developed by JSI medical systems GmbH JSI medical systems Corp. Tullastr. 18 One Boston Place, Suite 2600 77975 Ettenheim Boston, MA 02108 GERMANY

More information

UGENE Quick Start Guide

UGENE Quick Start Guide Quick Start Guide This document contains a quick introduction to UGENE. For more detailed information, you can find the UGENE User Manual and other special manuals in project website: http://ugene.unipro.ru.

More information

Leading Genomics. Diagnostic. Discove. Collab. harma. Shanghai Cambridge, MA Reykjavik

Leading Genomics. Diagnostic. Discove. Collab. harma. Shanghai Cambridge, MA Reykjavik Leading Genomics Diagnostic harma Discove Collab Shanghai Cambridge, MA Reykjavik Global leadership for using the genome to create better medicine WuXi NextCODE provides a uniquely proven and integrated

More information

Tutorial. Getting started with Ensembl Module 1 Introduction

Tutorial. Getting started with Ensembl  Module 1 Introduction Tutorial Getting started with Ensembl www.ensembl.org Ensembl provides genes and other annotation such as regulatory regions, conserved base pairs across species, and mrna protein mappings to the genome.

More information

Pairwise Sequence Alignment

Pairwise Sequence Alignment Pairwise Sequence Alignment carolin.kosiol@vetmeduni.ac.at SS 2013 Outline Pairwise sequence alignment global - Needleman Wunsch Gotoh algorithm local - Smith Waterman algorithm BLAST - heuristics What

More information

Cliquid ChemoView 3.0 Software Simple automated analysis, from sample to report

Cliquid ChemoView 3.0 Software Simple automated analysis, from sample to report PRODUCT BULLETIN Cliquid ChemoView 3.0 Software for Routine Screening and Quantitation Cliquid ChemoView 3.0 Software Simple automated analysis, from sample to report KEY FEATURES Secure user login that

More information

BIOLOMICS SOFTWARE & SERVICES GENERAL INFORMATION DOCUMENT

BIOLOMICS SOFTWARE & SERVICES GENERAL INFORMATION DOCUMENT BIOLOMICS SOFTWARE & SERVICES GENERAL INFORMATION DOCUMENT BIOAWARE SA NV - VERSION 2.0 - AUGUST 2013 BIOLOMICS SOFTWARE DYNAMIC CREATION AND MODIFICATION OF DATABASES Create simple or complex databases

More information

Creating Standard Curves with Genomic DNA or Plasmid DNA Templates for Use in Quantitative PCR

Creating Standard Curves with Genomic DNA or Plasmid DNA Templates for Use in Quantitative PCR Creating Standard Curves with Genomic DNA or Plasmid DNA Templates for Use in Quantitative PCR Overview Genomic DNA (gdna) and plasmids containing cloned target sequences are commonly used as standards

More information

Applied Biosystems 3500/3500xL Genetic Analyzer

Applied Biosystems 3500/3500xL Genetic Analyzer QUICK REFERENCE Applied Biosystems 3500/3500xL Genetic Analyzer with 3500 Series Data Collection Software 3 Catalog Number 4405186, 4405187 Pub. No. 100026299 Rev. A Note: For safety and biohazard guidelines,

More information

Monitor Mobile Devices via ActiveSync Using EventTracker

Monitor Mobile Devices via ActiveSync Using EventTracker Monitor Mobile Devices via ActiveSync Using EventTracker White Paper Publication Date: March 1, 2013 EventTracker 8815 Centre Park Drive Columbia MD 21045 www.eventtracker.com About This Guide Exchange

More information