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

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

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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Bibliographic Details
Main Authors: Argout, Xavier, Ruiz, Manuel, Fouet, Olivier, Lanaud, Claire, Wincker, Patrick, Da Silva, Corinne, Courtois, Brigitte
Format: conference_item biblioteca
Language:eng
Published: Cocoa Producers' Alliance
Subjects:F30 - Génétique et amélioration des plantes,
Online Access:http://agritrop.cirad.fr/549002/
http://agritrop.cirad.fr/549002/1/document_549002.pdf
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spelling dig-cirad-fr-5490022023-03-11T14:11:54Z http://agritrop.cirad.fr/549002/ http://agritrop.cirad.fr/549002/ 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. 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, 501-506. Conférence internationale sur la recherche cacaoyère. 15, San José, Costa Rica, 9 Octobre 2006/14 Octobre 2006. Researchers 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 eng 2010 Cocoa Producers' Alliance 15th International Cocoa Research Conference : cocoa productivity, quality, profitability, human health and the environment F30 - Génétique et amélioration des plantes 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. conference_item info:eu-repo/semantics/conferenceObject Conference info:eu-repo/semantics/publishedVersion http://agritrop.cirad.fr/549002/1/document_549002.pdf application/pdf Cirad license info:eu-repo/semantics/restrictedAccess https://agritrop.cirad.fr/mention_legale.html http://catalogue-bibliotheques.cirad.fr/cgi-bin/koha/opac-detail.pl?biblionumber=207299
institution CIRAD FR
collection DSpace
country Francia
countrycode FR
component Bibliográfico
access En linea
databasecode dig-cirad-fr
tag biblioteca
region Europa del Oeste
libraryname Biblioteca del CIRAD Francia
language eng
topic F30 - Génétique et amélioration des plantes
F30 - Génétique et amélioration des plantes
spellingShingle F30 - Génétique et amélioration des plantes
F30 - Génétique et amélioration des plantes
Argout, Xavier
Ruiz, Manuel
Fouet, Olivier
Lanaud, Claire
Wincker, Patrick
Da Silva, Corinne
Courtois, Brigitte
ESTtik, a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools
description 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.
format conference_item
topic_facet F30 - Génétique et amélioration des plantes
author Argout, Xavier
Ruiz, Manuel
Fouet, Olivier
Lanaud, Claire
Wincker, Patrick
Da Silva, Corinne
Courtois, Brigitte
author_facet Argout, Xavier
Ruiz, Manuel
Fouet, Olivier
Lanaud, Claire
Wincker, Patrick
Da Silva, Corinne
Courtois, Brigitte
author_sort Argout, Xavier
title ESTtik, a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools
title_short ESTtik, a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools
title_full ESTtik, a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools
title_fullStr ESTtik, a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools
title_full_unstemmed ESTtik, a semi-automatic cDNA sequence analysis and annotation pipeline including SSR and SNP search tools
title_sort esttik, a semi-automatic cdna sequence analysis and annotation pipeline including ssr and snp search tools
publisher Cocoa Producers' Alliance
url http://agritrop.cirad.fr/549002/
http://agritrop.cirad.fr/549002/1/document_549002.pdf
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AT ruizmanuel esttikasemiautomaticcdnasequenceanalysisandannotationpipelineincludingssrandsnpsearchtools
AT fouetolivier esttikasemiautomaticcdnasequenceanalysisandannotationpipelineincludingssrandsnpsearchtools
AT lanaudclaire esttikasemiautomaticcdnasequenceanalysisandannotationpipelineincludingssrandsnpsearchtools
AT winckerpatrick esttikasemiautomaticcdnasequenceanalysisandannotationpipelineincludingssrandsnpsearchtools
AT dasilvacorinne esttikasemiautomaticcdnasequenceanalysisandannotationpipelineincludingssrandsnpsearchtools
AT courtoisbrigitte esttikasemiautomaticcdnasequenceanalysisandannotationpipelineincludingssrandsnpsearchtools
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