Abstract
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. 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. Supplementary data are available at Bioinformatics online.
Highlights
Microsatellites are among the most informative and the most frequently used molecular markers in population biology
If several copies of the same loci are identified, and the sequencing was based on pooled DNA from several individuals, some of the null alleles can be detected and avoided if consensus sequence construction is stringent
Selection of sequences that have perfect microsatellites with a minimum number of repeats defined by the user. These sequences are written in a fasta file that will be the input for stage 2
Summary
Microsatellites are among the most informative and the most frequently used molecular markers in population biology. Their isolation for non-model species has been dependent on timeand labour-consuming laboratory protocols providing typically a few hundred sequences. The large number of sequences allows the detection of putative mobile elements by spotting sequence similarity groups and eliminating them. If several copies of the same loci are identified, and the sequencing was based on pooled DNA from several individuals, some of the null alleles can be detected and avoided if consensus sequence construction is stringent. QDD is designed to treat all bioinformatics steps from large quantities of raw sequences to the design of PCR primers for microsatellites amplification.
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