| GeneMark | |
| A family of gene prediction programs developed at Georgia Institute of Technology , Atlanta, Georgia, USA. |
| What's New: Publication on GeneMark-EP+ |
Supported by NIH  |
| 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. |
| Gene Prediction in Eukaryotes | |
| 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 | |
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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 . |
| 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:
For more information see Background and Publications. |
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