PDA: a pipeline to explore and estimate polymorphism in large DNA databases

Polymorphism studies are one of the main research areas of this genomic era. To date, however, no available web server or software package has been designed to automate the process of exploring and estimating nucleotide polymorphism in large DNA databases. Here, we introduce a novel software, PDA, Pipeline Diversity Analysis, that automatically can (i) search for polymorphic sequences in large databases, and (ii) estimate their genetic diversity. PDA is a collection of modules, mainly written in Perl, which works sequentially as follows: unaligned sequence retrieved from a DNA database are automatically classified by organism and gene, and aligned using the ClustalW algorithm. Sequence sets are regrouped depending on their similarity scores. Main diversity parameters, including polymorphism, synonymous and non-synonymous substitutions, linkage disequilibrium and codon bias are estimated both for the full length of the sequences and for specific functional regions. Program output includes a database with all sequences and estimations, and HTML pages with summary statistics, the performed alignments and a histogram maker tool. PDA is an essential tool to explore polymorphism in large DNA databases for sequences from different genes, populations or species. It has already been successfully applied to create a secondary database. PDA is available on the web at http://pda.uab.es/.