PolyPhred -- automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing
What you can do:
Compare fluorescence-based sequences across traces obtained from different individuals to identify heterozygous sites for single nucleotide substitutions.
Highlights:
- PolyPhred identifies potential heterozygotes using the base calls and peak information provided by Phred and the sequence alignments provided by Phrap.
- Potential heterozygotes identified by PolyPhred are marked for rapid inspection using the Consed tool.
- PolyPhred's functions are integrated with the use of three other programs: Phred, Phrap, and Consed.
- The current version 6 also helps automate detection and genotyping of indels (Structural and insertion-deletion variants) from sequence traces.
Keywords:
- heterozygous sites detection tool
- single nucleotide substitutions
- single nucleotide polymorphisms analysis tool
- SNPs analysis
- SNP analysis
- indels detection
- structural and insertion-deletion variants
- insertion-deletion polymorphisms detection
- genetic variation analysis
- heterozgyosity
- genotype
- genotyping
Literature & Tutorials:
PubMed Link of the original article (1997): PolyPhred -- automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing
PubMed Link of 2006 update: Automating resequencing-based detection of insertion-deletion polymorphisms
PubMed Link of 2006 update: Automating resequencing-based detection of insertion-deletion polymorphisms
This record last updated: 11-29-2006