After electrophoresis, data collection software creates a sample file of the raw data. Using downstream software applications, further data analysis is required to translate the collected color-data images into the corresponding nucleotide bases or fragment analysis allele cells.

Amplified fragments, along with appropriate size standards, migrate through a polymer-filled capillary and are detected using Data Collection Software (DCS). During an electrophoresis run, the DCS records the fluorescence intensity as a function of time and wavelength from regions on a CCD camera that correspond to different detection wavelength ranges. The resulting peaks are then processed according to the user-specified analysis parameters and size standard definition in the primary and secondary analysis software.

Primary Fragment Analysis

These tools convert the images gathered during Data Collection into sized fragment length peaks (Figure 2). For example, our Peak Scanner Software is a primary fragment analysis tool that can be used after data collection is completed. The Peak Scanner software application allows users to size, display, edit and print sample files. Primary fragment analysis software processes the raw data in an *.fsa file using algorithms and applies user-specified analysis settings to the results.

Secondary Fragment Analysis

These tools allow you to further refine your results. GeneMapper® Software is a flexible fragment analysis software package that provides quality DNA sizing and allele calls for all Applied Biosystems Genetic Analyzers. This software is designed to support multi-application functionality, including analysis of fragment length and/or number polymorphism applications, relative fluorescence quantitation applications, microsatellite and SNP genotyping applications, and conformation polymorphism applications. In addition to the functionality in primary fragment analysis, our secondary fragment analysis software (GeneMapper software) also performs a number of functions including allele calling and report table generation (Figure 3).

Product Selection Guide: Fragment Analysis Software for Data Analysis

Peak Scanner 2 (Download)
Primary Fragment Analysis Tool
  • Quickly analyze samples with the default sizing methods
  • View or print thumbnail and checkerboard view
  • View raw and analyzed data simultaneously
  • Analyze large fragments (e.g. 1200 bp)
  • View, edit, analyze, print, and export fragment analysis data
  • Fragment Analysis Applications
GeneMapper Software 6Primary and Secondary Analysis Tool
  • Security and audit features to help users meet 21 CFR Part 11 requirements
  • Report Manager tools for customized report generation
  • Definition of a linearity range in the analysis methods
  • Multiuser, client-server deployment
  • Ability to record and reapply the Size Standard Normalization factor calculated in 3500 Data Collection
  • Analysis of six-dye data from the Applied Biosystems® 3500 and 3500xL Series systems
  • Remote autoanalysis and command line operation
  • Process Quality Values (PQVs) for automated evaluation
  • Customization of the project autosaving frequency
  • Fragment Length/Number Polymorphism analysis
  • Large fragment analysis
  • Microsatellite/STR genotyping
  • Conformation analysis
  • Relative Fluorescence Quantitation analysis
  • SNP genotyping
  • Human identification for non-forensic use
  • Other applications, such as DNA Footprinting