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

Argout Xavier, Ruiz Manuel, Fouet Olivier, Lanaud Claire, Wincker Patrick, Da Silva Corinne, Courtois Brigitte. 2010. ESTtik, a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools. In : 15th International Cocoa Research Conference : cocoa productivity, quality, profitability, human health and the environment = 15e Conférence internationale sur la recherche cacaoyère : Productivité, qualité, rentabilité du cacao, santé humaine et environnement ; 15 Conferencia Internacional de Pesquisas em Cacau. Cacau : produtividade, qualidade, rentabilidade, saude humanna e amb. Lagos : Cocoa Producers' Alliance, pp. 501-506. Conférence internationale sur la recherche cacaoyère. 15, San José, Costa Rica, 9 October 2006/14 October 2006.

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Titre français : ESTtik, un pipeline d'analyse et d'annotation semi-automatique de séquences ADN pour la génération d'ADNc comprenant une recherche de SSR et de SNP / Titre portugais : ESTtik, uma análise de sequência de ADN semi-automática e anotação em cadeia para geração de cADN incluindo busca SSR e SNP / Titre espagnol : ESTtik, un análisis de secuencia de ADN semiautomático y un pipeline de anotación para generación de cADN incluyendo búsqueda de SSR y SNP

Abstract : 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. (Résumé d'auteur)

Classification Agris : F30 - Plant genetics and breeding

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