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Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases

AuthorsXavier, D.; Rodríguez, J. M.; Moran, F.; Crespo, Berta ; Gómez, Ana ; Ribas, Laia ; Piferrer, Francesc
Issue DateJan-2012
CitationXI Jornadas de Bioinformática book of abstracts: P62 (2012)
AbstractSea bass (Dicentrarchus labrax) is one of the most relevant fish for marine aquaculture in Spain and has been extensively studied by Aquagenomics Project (http://www.aquagenomics.es). In this work, we present the annotation and curation pipeline developed to functionally annotate sea bass transcriptome. The genetic data was obtained from two cDNA libraries of gonads at different stages of maturation by experimental groups of Aquagenomics Project (IATS and ICM, CSIC, Spain). The 454 sequencing was performed in the Max Planck Institute for Molecular Genetics and the obtained reads were assembled with MIRA [1], yielding a total of 32,427 contigs. The annotation was carried out with respect to model fishes from Ensembl [2] database (Danio rerio, Tetraodon nigroviridis, Gasterosteus aculeatus, Oryzias latipes, Takifugu rubripes) and NCBI [3] noredundant protein database. For both databases, we performed BLAST [4] searches to distinguish the different threshold levels of gene/protein homology. Besides, the pipeline executes PfamScan [5] algorithm and RPS-BLAST against NCBI Conserved Domains Database [6] to detect possible protein domains. Finally, genes were mapped to Gene Ontology (GO) terms [7] using cross-reference data from Gene Ontology, NCBI, Ensembl and UniProt [8] databases, and also through BLAST2GO [9] software. The curation process was developed based on rules that give different scores to each decision and take into account aspects such as the existence of domains, the conservation of the active sites, e-value, identity percentage, and homology length. The results from annotation and curation will be presented and discussed in terms of their application to DNA-microarray design in the framework of the Aquagenomics Projec
DescriptionXI Jornadas de Bioinformática, 23-25 January 2012 Barcelona
Publisher version (URL)http://sgt.cnag.cat/jbi2012/
Appears in Collections:(ICM) Comunicaciones congresos
(IATS) Comunicaciones congresos
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