Abstract
The iBeetle-Base provides access to sequence and phenotype information for genes of the beetle Tribolium castaneum. It has been updated including more and updated data and new functions. RNAi phenotypes are now available for >50% of the genes, which represents an expansion of 60% compared to the previous version. Gene sequence information has been updated based on the new official gene set OGS3 and covers all genes. Interoperability with FlyBase has been enhanced: First, gene information pages of homologous genes are interlinked between both databases. Second, some steps of a new query pipeline allow transforming gene lists from either species into lists with related gene IDs, names or GO terms. This facilitates the comparative analysis of gene functions between fly and beetle. The backend of the pipeline is implemented as endpoints of a RESTful interface, such that it can be reused by other projects or tools. A novel online interface allows the community to propose GO terms for their gene of interest expanding the range of animals where GO terms are defined. iBeetle-Base is available at http://ibeetle-base.uni-goettingen.de/
Highlights
With the advent of generation sequencing (NGS) the number of species with a sequenced genome or transcriptome is rapidly increasing and comprehensive inventories of genes become available for more and more taxa
The initial dataset of iBeetle-Base was the result of the first phase of the unbiased large scale RNAi screen iBeetle performed in the red flour beetle T. castaneum [6,7]
The homology assignments for this release have been calculated by OrthoDB based on version 9, using FlyBase release April 2015 [13]
Summary
With the advent of generation sequencing (NGS) the number of species with a sequenced genome or transcriptome is rapidly increasing and comprehensive inventories of genes become available for more and more taxa. Phenotypic data for approximately 30% of the genes was gathered during this project and was published at iBeetle-Base along with respective gene sequence information. A new query pipeline was implemented that allows transforming lists of gene IDs of either fly or beetle into other IDs and allows retrieving additional information like gene names and GO terms.
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