SeqScape Software Version 2.1 User Guide - InfoNet

Chapter 1
Introduction to ABI PRISM SeqScape Software
Data Sources for
Resequencing
Projects
Levels of
Automated
Analysis
What the
Software Does
You can create projects in SeqScape software using sequencing data
generated from the following systems:
• ABI PRISM ® 310 Genetic Analyzer
• ABI PRISM ® 377 DNA Sequencer
• ABI PRISM ® 3100-Avant Genetic Analyzer
• ABI PRISM ® 3100 Genetic Analyzer
• ABI PRISM ® 3700 DNA Analyzer
• Applied Biosystems 3730 DNA Analyzer
• Applied Biosystems 3730xl DNA Analyzer
Each project can contain:
• Unanalyzed sample files (.ab1)
• Previously basecalled sample files (.ab1)
• Text sequences (.seq or .fsta)
• Aligned consensus sequences
A single project can contain sample files from one or a mixture of
instrument platforms. The software analyzes the data, displays
several views of the analyzed project, and reports on results for
quality control and data review.
SeqScape software performs two levels of analysis:
• It identifies variants, positions that differ from the reference
sequence, and classifies those variants as known or unknown.
• It searches a library of alleles or haplotypes to identify the
alleles that most closely match the sample.
When you have added a reference sequence, a library, and sample
files, SeqScape software performs two levels of analysis:
• Identification of nucleotide and amino acid variants.The
software identifies positions that differ from the reference
sequence and classifies those variants as known or unknown
variants.
• Identification of genotypes, alleles, or haplotypes from a library.
In addition to identification of variants, the software searches a
library of genotypes, alleles, or haplotypes and identifies the
alleles that most closely match each consensus sequence.
1-6 ABI PRISM SeqScape Software v2.1 User Guide
DRAFT
August 28, 2003 2:54 pm, 1_Intro.fm