Abstract
The Whole Transcriptome Shotgun Sequencing (RNA-seq) uses the Next Generation Sequencing (NGS) capabilities to analyze RNA transcript counts and their quantification, with an extraordinary accuracy. In order to provide a comprehensive knowledge about the non-reference model organism Hydra vulgaris water polyp, we developed a comprehensive database in which the whole functional annotated transcriptome is integrated, and from which it is possible to have access and download all the information related to 15,522 transcripts. The study includes different functional annotations coming from 19 repositories, conveniently grouped by type, such as: i. Pathway: BBID, BioCarta, KEGG, Panther; ii. Domain: COG-Ontology, Interpro, PIR Superfamily, SMART, PFam; iii. Protein Interaction: BIND, MINT, UCSF-TFBS; iv. GO: GO-Term Cellular Components, GO-Term Biological Processes, GO-Term Molecular Functions; v. Miscellaneous: OMIM, EC Number, SP-PIR Keywords, UP-SEQ features. The easily-accessible nature of HvDBase makes this resource a valuable tool for rapidly retrieve knowledges at transcript level as well as useful to inspect differential expression of protein-coding genes in Hydra vulgaris transcriptome in the contex to the different experimental condition. Web resource URL: http://www-labgtp.na.icar.cnr.it/HvDBase
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Evangelista, D., Tripathi, K.P., Scuotto, V., Guarracino, M.R. (2015). HvDBase: A Web Resource on Hydra Vulgaris Transcriptome. In: Ortuño, F., Rojas, I. (eds) Bioinformatics and Biomedical Engineering. IWBBIO 2015. Lecture Notes in Computer Science(), vol 9044. Springer, Cham. https://doi.org/10.1007/978-3-319-16480-9_35
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DOI: https://doi.org/10.1007/978-3-319-16480-9_35
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