PDA

PDA automates detection and analysis of DNA sequence polymorphisms to estimate genetic diversity parameters and organize sequences for polymorphism database construction.

Key Features:

• Automated polymorphism detection: Identifies polymorphic sequences within large DNA database retrievals.
• Sequence retrieval and classification: Retrieves unaligned sequences from DNA databases and classifies them by organism and gene.
• Multiple sequence alignment: Performs alignments using the ClustalW algorithm.
• Sequence grouping: Regroups sequence sets based on similarity scores for downstream analysis.
• Genetic diversity estimation: Estimates polymorphism levels, synonymous and non-synonymous substitutions, linkage disequilibrium, and codon bias for full-length sequences and specific functional regions.
• Quality assessment criteria: Applies criteria to assess data quality for polymorphism analyses.
• Output generation and visualization: Produces a comprehensive sequence database, HTML summary pages with alignments and statistics, and histogram visualizations.
• Implementation: Implemented as a collection of modules primarily written in Perl.

Scientific Applications:

• Polymorphism database construction: Enables creation of secondary polymorphism databases such as the Drosophila Polymorphism Database (DPDB).
• Population genetics and molecular evolution: Supports analysis of genetic variation across genes, populations, and species to study evolutionary processes, population genetics, and molecular evolution.
• Comparative sequence analyses: Facilitates comparative analyses of sequence diversity within and between taxa and functional regions.

Methodology:

PDA is implemented as Perl modules that retrieve unaligned sequences from DNA databases, classify them by organism and gene, align sequences with ClustalW, regroup sets by similarity scores, and estimate diversity parameters such as polymorphism levels, synonymous/non-synonymous substitutions, linkage disequilibrium, and codon bias.