MetaGeneMark-2: Improved Gene Prediction in Metagenomes

Abstract

AbstractAccurate prediction of protein-coding genes in metagenomic contigs presents a well-known challenge. Particularly difficult is to identify short and incomplete genes as well as positions of translation initiation sites. It is frequently assumed that initiation of translation in prokaryotes is controlled by a ribosome binding site (RBS), a sequence with the Shine-Dalgarno (SD) consensus situated in the 5’ UTR. However, ∼30% of the 5,007 genomes, representing the RefSeq collection of prokaryotic genomes, have either non-SD RBS sequences or no RBS site due to physical absence of the 5’ UTR (the case of leaderless transcription). Predictions of the gene 3’ ends are much more accurate; still, errors could occur due to the use of incorrect genetic code. Hence, an effective gene finding algorithm would identify true genetic code in a process of the sequence analysis. In this work prediction of gene starts was improved by inferring the GC content dependent generating functions for RBS sequences as well as for promoter sequences involved in leaderless transcription. An additional feature of the algorithm was the ability to identify alternative genetic code defined by a reassignment of the TGA stop codon (the only stop codon reassignment type known in prokaryotes). It was demonstrated that MetaGeneMark-2 made more accurate gene predictions in metagenomic sequences than several existing state-of-the-art tools.