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ESTtik, a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools

Argout X., Ruiz M., Fouet O., Lanaud C., Wincker P., Da Silva C., Courtois B.. 2010. In : 15th International Cocoa Research Conference : cocoa productivity, quality, profitability, human health and the environment. Lagos : Cocoa Producers' Alliance, p. 501-506. Conférence internationale sur la recherche cacaoyère. 15, 2006-10-09/2006-10-14, San José (Costa Rica).

The Expressed Sequence Tag Treatment and Investigation Kit project (ESTtik) was initiated to analyse and store results from processing of cDNA. To this end, a semi automatic pipeline for analysis and annotation of sequences, as well as a relational database developed for the storage of information related to the treatment, were deployed. The pipeline successively performs base calling, vector trimming, assembly and functional annotation. The non redundant data are then mined for Simple Sequence Repeat (SSR) markers and three primer pairs for each SSR found are designed. Single Nucleotide Polymorphisms (SNPs) are also detected. Data from the pipeline are systematically stored in a relational database, searchable via a local Web browser-based interface. This tool allows complex queries of the data to explore the expressed genes.

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