RNAcode_Web – Convenient identification of evolutionary conserved protein coding regions

Abstract

The differentiation of regions with coding potential from non-coding regions remains a key task in computational biology. Methods such as RNAcode that exploit patterns of sequence conservation for this task have a substantial advantage in classification accuracy in particular for short coding sequences, compared to methods that rely on a single input sequence. However, they require sequence alignments as input. Frequently, suitable multiple sequence alignments are not readily available and are tedious, and sometimes difficult to construct. We therefore introduce here a new web service that provides access to the well-known coding sequence detector RNAcode with minimal user overhead. It requires as input only a single target nucleotide sequence. The service automates the collection, selection, and preparation of homologous sequences from the NCBI database, as well as the construction of the multiple sequence alignment that are needed as input for RNAcode. The service automatizes the entire pre- and postprocessing and thus makes the investigation of specific genomic regions for previously unannotated coding regions, such as small peptides or additional introns, a simple task that is easily accessible to non-expert users. RNAcode_Web is accessible online at rnacode.bioinf.uni-leipzig.de.

The Cryptic Bacterial Microproteome

“…To predict which ismORFs encoded putative microproteins in enterobacterial genomes, two computational methods were employed, RNAcode tool 31,32 and modified EvolScore 5 , both based on the estimation of selective constraints (see STAR Methods for details). RNAcode was recently used to identify functional small proteins in metagenomic analysis 11,33 .…”