Publications des agents du Cirad


SAT, a web-based pipeline for SSR markers development from enriched libraries

Dereeper A., Argout X., Billot C., Rami J.F., Ruiz M.. 2006. In : Abstracts of Plant and Animal Genomes XIVth Conference, San Diego, CA (USA), January 14-18, 2006. s.l. : s.n.. Plant and Animal Genomes Conference. 14, 2006-01-14/2006-01-18, San Diego (Etats-Unis).

Analysis of sequences obtained from SSR (Simple Sequence Repeat) enriched libraries has been shown to exhibit difficulties that are not taken into consideration for other type of sequences (EST, BAC etc...), and are thus difficult for scientists to integrate and deal with. In this context, SAT (SSR Analysis Tool) has been designed to help minimize tedious manual operations, to reduce the level of errors, and to facilitate the tasks of integrating, analyzing and managing nucleotide sequences coming from SSR libraries. SAT is a user-friendly web-based system designed to successively perform base-calling and quality evaluation of chromatograms, vector and adaptors removing, restriction digestion (in order to separate the DNA fragments which could have formed chimera during the process of library construction), SSR recognition, clustering and alignment, and finally primer design on consensus sequences. An additional virtual PCR completes the treatment in establishing primer specificity. Although there is an obligatory kernel of tasks (SSR recognition and sequence alignment), the user is not constrained to run the entire treatment and can choose the steps to perform. It can thus be applied to other type of sequences than those obtained from SSR enriched libraries. The pipeline is associated to a MySQL database to store the different steps of the run, and to reprocess some further analysis on the consensus sequences and their respective primers (specificity, refinement of the alignment, sequences without primers, etc). (Texte intégral)
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