GeneMark  
  A family of gene prediction programs developed at Georgia Institute of Technology , Atlanta, Georgia, USA.
What's New: A new algorithm, GeneMark-ET , an automatically trained eukaryotic gene finder utilizing mapped RNA-Seq reads was published in NAR. Supported by NIH
NIH

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 the program GeneMark-ES utilizing unsupervised training. Note that GeneMark-ES has a special mode for analyzing fungal genomes. Recently, we have developed a semi-supervised version of GeneMark-ES, called GeneMark-ET that uses RNA-Seq reads to improve training. For several species pre-trained model parameters are ready and available through the GeneMark.hmm page.
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 : an annotation pipeline and genome-database management tool for second-generation genome projects
    -- using GeneMark-ES

For more information see Background and Publications.

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