GeneMark-HM: improving gene prediction in DNA sequences of human microbiome.

ABSTRACT: Computational reconstruction of nearly complete genomes from metagenomic reads may identify thousands of new uncultured candidate bacterial species. We have shown that reconstructed prokaryotic genomes along with genomes of sequenced microbial isolates can be used to support more accurate gene prediction in novel metagenomic sequences. We have proposed an approach that used three types of gene prediction algorithms and found for all contigs in a metagenome nearly optimal models of protein-coding regions either in libraries of pre-computed models or constructed de novo. The model selection process and gene annotation were done by the new GeneMark-HM pipeline. We have created a database of the species level pan-genomes for the human microbiome. To create a library of models representi

SUBMITTER: Lomsadze A 

PROVIDER: S-EPMC8153819 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature