Journal Article

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

Emese Meglécz, Caroline Costedoat, Vincent Dubut, André Gilles, Thibaut Malausa, Nicolas Pech and Jean-François Martin

in Bioinformatics

Volume 26, issue 3, pages 403-404
Published in print February 2010 | ISSN: 1367-4803
Published online December 2009 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btp670
QDD: a user-friendly program to select microsatellite markers and design primers from large sequencing projects

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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 hundred base pairs in the tag-sorting step, and up to 50 000 sequences in a single input file for the steps involving estimation of sequence similarity.

Availability: QDD is freely available under the GPL licence for Windows and Linux from the following web site: http://www.univ-provence.fr/gsite/Local/egee/dir/meglecz/QDD.html

Contact: emese.meglecz@univ-provence.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1202 words. 

Subjects: Bioinformatics and Computational Biology

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