GeneMark-EP+: eukaryotic gene prediction with self-training in the space of genes and proteins.

ABSTRACT: We have made several steps toward creating a fast and accurate algorithm for gene prediction in eukaryotic genomes. First, we introduced an automated method for efficient ab initio gene finding, GeneMark-ES, with parameters trained in iterative unsupervised mode. Next, in GeneMark-ET we proposed a method of integration of unsupervised training with information on intron positions revealed by mapping short RNA reads. Now we describe GeneMark-EP, a tool that utilizes another source of external information, a protein database, readily available prior to the start of a sequencing project. A new specialized pipeline, ProtHint, initiates massive protein mapping to genome and extracts hints to splice sites and translation start and stop sites of potential genes. GeneMark-EP uses the

SUBMITTER: Bruna T 

PROVIDER: S-EPMC7222226 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature