Institute of Bioinformatics WWU Münster
Curation Process

For uORFdb version 1.0, a Boolean search for "upstream open reading" OR "uORF" OR "uORFs" OR "upstream initiation" OR "uAUG" OR "small open reading" OR "sORF" OR "upORF" OR "ribosome profiling" was applied to the NCBI PubMed database at Pubmed on 15 July 2013. This search returned a total of 981 publications. The articles were curated manually to eliminate non-related accidental hits. Furthermore, only publications investigating eukaryotic or viral transcripts/uORFs were included, while bacterial data was omitted. The remaining 467 individual publications were categorized according to the type of article, the taxon and transcript analyzed, and the individual uORF properties investigated. Wherever possible, the taxon, gene or nucleotide accession number was extracted from the literature and linked to the corresponding NCBI database [PMID:23193264].

The uORFdb permits filtering publications for individual or multiple numerical, structural, sequential, and co-factor-related features, facilitating convenient access to the complex field of uORF-mediated translational control mechanisms.