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

ABSTRACT: 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 polymorphis

SUBMITTER: Casillas S 

PROVIDER: S-EPMC441566 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature