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dc.contributor.authorChou, Chih-Hungen_US
dc.contributor.authorHuang, Hsi-Yuanen_US
dc.contributor.authorHuang, Wei-Chihen_US
dc.contributor.authorHsu, Sheng-Daen_US
dc.contributor.authorHsiao, Chung-Deren_US
dc.contributor.authorLiu, Chia-Yuen_US
dc.contributor.authorChen, Yu-Hungen_US
dc.contributor.authorLiu, Yu-Chenen_US
dc.contributor.authorHuang, Wei-Yunen_US
dc.contributor.authorLee, Meng-Linen_US
dc.contributor.authorChen, Yi-Changen_US
dc.contributor.authorHuang, Hsien-Daen_US
dc.date.accessioned2018-08-21T05:53:38Z-
dc.date.available2018-08-21T05:53:38Z-
dc.date.issued2018-05-09en_US
dc.identifier.issn1471-2164en_US
dc.identifier.urihttp://dx.doi.org/10.1186/s12864-018-4463-xen_US
dc.identifier.urihttp://hdl.handle.net/11536/144966-
dc.description.abstractBackground: Aquatic animals have great economic and ecological importance. Among them, non-model organisms have been studied regarding eco-toxicity, stress biology, and environmental adaptation. Due to recent advances in next-generation sequencing techniques, large amounts of RNA-seq data for aquatic animals are publicly available. However, currently there is no comprehensive resource exist for the analysis, unification, and integration of these datasets. This study utilizes computational approaches to build a new resource of transcriptomic maps for aquatic animals. This aquatic animal transcriptome map database dbATM provides de novo assembly of transcriptome, gene annotation and comparative analysis of more than twenty aquatic organisms without draft genome. Results: To improve the assembly quality, three computational tools (Trinity, Oases and SOAPdenovo-Trans) were employed to enhance individual transcriptome assembly, and CAP3 and CD-HIT-EST software were then used to merge these three assembled transcriptomes. In addition, functional annotation analysis provides valuable clues to gene characteristics, including full-length transcript coding regions, conserved domains, gene ontology and KEGG pathways. Furthermore, all aquatic animal genes are essential for comparative genomics tasks such as constructing homologous gene groups and blast databases and phylogenetic analysis. Conclusion: In conclusion, we establish a resource for non model organism aquatic animals, which is great economic and ecological importance and provide transcriptomic information including functional annotation and comparative transcriptome analysis.en_US
dc.language.isoen_USen_US
dc.titleThe aquatic animals' transcriptome resource for comparative functional analysisen_US
dc.typeArticleen_US
dc.identifier.doi10.1186/s12864-018-4463-xen_US
dc.identifier.journalBMC GENOMICSen_US
dc.citation.volume19en_US
dc.citation.issue2en_US
dc.contributor.department生物科技學系zh_TW
dc.contributor.department生物資訊及系統生物研究所zh_TW
dc.contributor.department分子醫學與生物工程研究所zh_TW
dc.contributor.departmentDepartment of Biological Science and Technologyen_US
dc.contributor.departmentInstitude of Bioinformatics and Systems Biologyen_US
dc.contributor.departmentInstitute of Molecular Medicine and Bioengineeringen_US
dc.identifier.wosnumberWOS:000431831100014en_US
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