articleBioinformaticsDec 10, 2009HYBRID OA

QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects

EMEmese MegléczCCCaroline CostedoatVDVincent DubutAGAndré GillesTMThibaut Malausa

Centre National de la Recherche Scientifique · Centre de Coopération Internationale en Recherche Agronomique pour le Développement · +4 more institutions

PubMed
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Abstract

SUMMARY: QDD is an open access program providing a user-friendly tool for microsatellite detection and primer design from large sets of DNA sequences. The program is designed to deal with all steps of treatment of raw sequences obtained from pyrosequencing of enriched DNA libraries, but it is also applicable to data obtained through other sequencing methods, using FASTA files as input. The following tasks are completed by QDD: tag sorting, adapter/vector removal, elimination of redundant sequences, detection of possible genomic multicopies (duplicated loci or transposable elements), stringent selection of target microsatellites and customizable primer design. It can treat up to one million sequences of a few…

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Topics & keywords

Topics
Keywords
  • Adapter (computing)
  • Microsatellite
  • Computer science
  • Primer (cosmetics)
  • DNA sequencing
  • Computational biology
  • Biology
  • Genetics
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