Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes |
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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.
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Gene Prediction in Eukaryotes |
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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.
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Gene Prediction in Transcripts |
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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 .
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Gene Prediction in Viruses, Phages and Plasmids |
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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.
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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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