Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases
XI Jornadas de Bioinformática, 23-25 January 2012 Barcelona
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dig-icm-es-10261-806812019-06-28T08:46:14Z Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases Xavier, D. Rodríguez, J. M. Morán, F. Crespo, Berta Gómez, Ana Ribas, Laia Piferrer, Francesc XI Jornadas de Bioinformática, 23-25 January 2012 Barcelona Sea 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 This work has been supported by Grant CSD2007-00002 Consolider-Ingenio 2010, MICINN (Spain) Peer Reviewed 2012-01 2013-08-19T10:13:03Z comunicación de congreso http://purl.org/coar/resource_type/c_5794 XI Jornadas de Bioinformática book of abstracts: P62 (2012) http://hdl.handle.net/10261/80681 en http://sgt.cnag.cat/jbi2012/ none |
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English |
| description |
XI Jornadas de Bioinformática, 23-25 January 2012 Barcelona |
| format |
comunicación de congreso |
| author |
Xavier, D. Rodríguez, J. M. Morán, F. Crespo, Berta Gómez, Ana Ribas, Laia Piferrer, Francesc |
| spellingShingle |
Xavier, D. Rodríguez, J. M. Morán, F. Crespo, Berta Gómez, Ana Ribas, Laia Piferrer, Francesc Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases |
| author_facet |
Xavier, D. Rodríguez, J. M. Morán, F. Crespo, Berta Gómez, Ana Ribas, Laia Piferrer, Francesc |
| author_sort |
Xavier, D. |
| title |
Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases |
| title_short |
Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases |
| title_full |
Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases |
| title_fullStr |
Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases |
| title_full_unstemmed |
Annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases |
| title_sort |
annotation pipeline for 454 assembly of sea bass gonads using model fishes and other databases |
| url |
http://hdl.handle.net/10261/80681 |
| work_keys_str_mv |
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