PDA -- A Pipeline to Explore and Estimate Polymorphism in Large DNA databases

URL:
http://pda.uab.es/
What you can do:
Search for polymorphic sequences in large databases and estimate their genetic diversity.
Highlights:
  • PDA 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.
  • 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.
  • The 2006 release PDA v.2 adds new methods for data mining and grouping sequences, new criteria for data quality assessment and a better user interface.
Keywords:
  • polymorphism
  • SNPs
  • SNPs search tool
  • synonymous substitutions
  • non-synonymous substitutions
Literature & Tutorials:
PubMed Link: PDA -- A Pipeline to Explore and Estimate Polymorphism in Large DNA databases
PubMed Link of 2006 update: PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA
This record last updated: 08-03-2006
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