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


BACKGROUND
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.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Meglécz
Emese
E
Aix-Marseille Université, CNRS, IRD, UMR 6116-IMEP, Equipe Evolution, Génome et Environnement, Centre Saint-Charles, Case 36, 3 Place Victor Hugo, 13331 Marseille Cedex 3, France. emese.meglecz@univ-provence.fr
Costedoat
Caroline
C
Dubut
Vincent
V
Gilles
André
A
Malausa
Thibaut
T
Pech
Nicolas
N
Martin
Jean-François
JF
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D017931:DNA Primers / Q000737:chemistry*; D030541:Databases, Genetic; D018895:Microsatellite Repeats; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D017931:DNA Primers