SAT, a flexible and optimized Web application for SSR marker development.

Dereeper Alexis, Argout Xavier, Billot Claire, Rami Jean-François, Ruiz Manuel. 2007. SAT, a flexible and optimized Web application for SSR marker development.. BMC Bioinformatics, 8 (465), 10 p.

https://doi.org/10.1186/1471-2105-8-465

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Résumé : Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched for SSR sequences, followed by DNA sequencing. However, designing optimal SSR markers from bulk sequence data is a laborious and time-consuming process. RESULTS: SAT (SSR Analysis Tool) is a user-friendly Web application developed to minimize tedious manual operations and reduce errors. This tool facilitates the integration, analysis and display of sequence data from SSR-enriched libraries. SAT is designed to successively perform base calling and quality evaluation of chromatograms, eliminate cloning vector, adaptors and low quality sequences, detect chimera or partially digested sequences, search for SSR motifs, cluster and assemble the redundant sequences, and design SSR primer pairs. An additional virtual PCR step establishes primer specificity. Users may modify the different parameters of each step of the SAT analysis. Although certain steps are compulsory, such as SSR motifs search and sequence assembly, users do not have to run the entire pipeline, and they can choose selectively which steps to perform. A database allows users to store and query results, and to redo individual steps of the workflow. CONCLUSIONS: The SAT Web application is available at http://sat.cirad.fr/sat, and a standalone command-line version is also freely downloadable. Users must send an email to the SAT administrator (tropgene@cirad.fr) to request a login and password.

Mots-clés Agrovoc : système d'information, marqueur génétique, microsatellite, génie génétique, banque de gènes, banque de données, application des ordinateurs, Sorghum

Mots-clés complémentaires : SSR

Classification Agris : F30 - Génétique et amélioration des plantes
C30 - Documentation et information
U10 - Informatique, mathématiques et statistiques

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

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