RiboSeqDB – a repository of selected human and mouse ribosome footprint and RNA-seq data

Abstract

Motivation: At present time, there are many different data sets obtained as the results of ribosome profiling and RNA-seq experiments worldwide. Those data sets, mainly, are collected at public databases like Gene Expression Omnibus (GEO) and Short Read Archive (SRA) that are rather huge and some inconveniences with navigation and search exist there. So, for our work dedicated to analysis of different aspects of genome information realization like preference of different transcription starts, influence of different nucleotide motifs on translation efficacy in human and mouse we looked through and selected a range of datasets on common cell lines. Selected datasets will be stored with the results of our calculations on translation efficacy performed during the project using a BioUML platform.

Results: For storage and analysis of the selected from different sources datasets, a RiboSeqDB database was created. Currently, our database comprising 290 data samples of 21 datasets for human and mouse is being further developed acquiring new features and possibilities for users in navigation, data processing and analysis.