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

By Emese Meglécz, Caroline Costedoat, V. Dubut, André Gilles, Thibaut Malausa, Nicolas Pech, Jean-François Martin. Bioinform., 2010

604 citations recorded by the source corpus.

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. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0fdcbf47d720d7da45d743c1a7bafac94e024367

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In Genetics

1. R. Petit
2. M. Cock
3. S. Wagner
4. Olivier Lepais
5. Thibaut Malausa
6. Philippe Chaumeil
7. E. Guichoux
8. J. Gaskin

In Molecular Biology

1. R. Petit
2. S. Wagner
3. Olivier Lepais
4. Thibaut Malausa
5. Philippe Chaumeil
6. E. Guichoux
7. F. Salin
8. P. Léger

Citations in the corpus

• Applying molecular-based approaches to classical biological control of weeds (2011, methodology): “Concomitantly, new bioinformatic tools have been developed for microsatellite detection and primer design from such larger sets of sequences (Meglecz et al., 2010).”
• Current trends in microsatellite genotyping (2011, methodology): “Software, such as MSATCOMMANDER (Faircloth 2008) or QDD (Meglécz et al. 2010), has been created to identify SSRs from 454 sequence data, the first one being used in more than half of the studies.”
• Methods for Development of Microsatellite Markers: An Overview (2014, neutral): “…SSR mining tools like TROLL (Castelo et al., 2002), MISA (Thiel et al., 2003), SciRoKo (Kofler et al., 2007), Msatcommander (Faircloth, 2008), QDD (Meglécz et al., 2010) etc., it has now become a fast approach to search for microsatellite repeats in the EST sequences/ databases and exploit the…”