A family of gene prediction programs developed at Georgia Institute of Technology , Atlanta, Georgia, USA.
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Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes
circular genome Novel genomic sequences can be analyzed either by the self-training program GeneMarkS (sequences longer than 50 kb) or by GeneMark.hmm with Heuristic models. For many species pre-trained model parameters are ready and available through the GeneMark.hmm page. Metagenomic sequences can be analyzed by MetaGeneMark , the program optimized for speed.
Gene Prediction in Eukaryotes
mouse Novel genomes can be analyzed by GeneMark-ES, an algorithm utilizing models parameterized by unsupervised training. Notably, GeneMark-ES has a special option for fungal genomes to account for fungal-specific intron organization. To integrate into GeneMark-ES information on mapped RNA-Seq reads, we made semi-supervised GeneMark-ET. Recently, we have developed GeneMark-EP+ that uses homologous protein sequences of any evolutionary distance in both training and predictions.
Gene Prediction in Transcripts
gel Sets of assembled eukaryotic transcripts can be analyzed by the modified GeneMarkS algorithm (the set should be large enough to permit self-training). A single transcript can be analyzed by a special version of GeneMark.hmm with Heuristic models. A new advanced algorithm GeneMarkS-T was developed recently (manuscript sent to publisher); The GeneMarkS-T software (beta version) is available for download .
Gene Prediction in Viruses, Phages and Plasmids
virus Sequences of viruses, phages or plasmids can be analyzed either by the GeneMark.hmm with Heuristic models (if the sequence is shorter than 50 kb) or by the self-training program GeneMarkS.

All the software programs mentioned here are available for download and local installation.

The software of GeneMark line is a part of genome annotation pipelines at NCBI, JGI, Broad Institute as well as the following software packages:
  • QUAST : quality assessment tool for genome assemblies
    -- using GeneMarkS
  • MetAMOS : a modular and open source metagenomic assembly and analysis
    -- using MetaGeneMark
  • MAKER2 : a eukaryotic genome annotation pipeline
    -- using GeneMark-ES (along with SNAP and AUGUSTUS)
  • BRAKER1: an RNA-seq based eukaryotic genome annotation pipeline
    -- using GeneMark-ET and AUGUSTUS
  • BRAKER2: an Protein based eukaryotic genome annotation pipeline
    -- using GeneMark-EP+ and AUGUSTUS

For more information see Background and Publications.

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