StartLink and StartLink+: Prediction of Gene Starts in Prokaryotic Genomes.

ABSTRACT: State-of-the-art algorithms of ab initio gene prediction for prokaryotic genomes were shown to be sufficiently accurate. A pair of algorithms would agree on predictions of gene 3'ends. Nonetheless, predictions of gene starts would not match for 15-25% of genes in a genome. This discrepancy is a serious issue that is difficult to be resolved due to the absence of sufficiently large sets of genes with experimentally verified starts. We have introduced StartLink that infers gene starts from conservation patterns revealed by multiple alignments of homologous nucleotide sequences. We also have introduced StartLink+ combining both ab initio and alignment-based methods. The ability of StartLink to predict the start of a given gene is restricted by the availability of homologs in a d

SUBMITTER: Gemayel K 

PROVIDER: S-EPMC9581028 | biostudies-literature | 2021

REPOSITORIES: biostudies-literature