PDA v.2: improving the exploration and estimation of nucleotide polymorphism in large datasets of heterogeneous DNA

Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (D...

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Bibliographic Details
Published in:Nucleic acids research 2006-07, Vol.34 (suppl-2), p.W632-W634
Main Authors: Casillas, Sònia, Barbadilla, Antonio
Format: Article
Language:English
Subjects:
Algorithms
Animals
Databases, Nucleic Acid
DNA
Drosophila
Drosophila - genetics
genetic polymorphism
genetic variation
Internet
Internet resource
new methods
nucleotides
Polymorphism, Genetic
Quality Control
Sequence Alignment - standards
Sequence Analysis, DNA - methods
Software - standards
user interface
User-Computer Interface
world wide web
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Description
Summary:Pipeline Diversity Analysis (PDA) is an open-source, web-based tool that allows the exploration of polymorphism in large datasets of heterogeneous DNA sequences, and can be used to create secondary polymorphism databases for different taxonomic groups, such as the Drosophila Polymorphism Database (DPDB). A new version of the pipeline presented here, PDA v.2, incorporates substantial improvements, including new methods for data mining and grouping sequences, new criteria for data quality assessment and a better user interface. PDA is a powerful tool to obtain and synthesize existing empirical evidence on genetic diversity in any species or species group. PDA v.2 is available on the web at http://pda.uab.es/.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkl080