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GeneMark specifications

Information


Unique identifier OMICS_01485
Name GeneMark
Alternative name GeneMark-ES
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Input data A sequence.
Input format FASTA
Output format A protein sequence or a gene nucleotide sequence.
Operating system Unix/Linux
Computer skills Basic
Version 2.5
Stability Stable
Maintained Yes

Subtool


  • bfgf

Versioning


No version available

Documentation


Maintainers


  • person_outline Mark Borodovsky
  • person_outline Alex Lomsadze

Publication for GeneMark

GeneMark citations

 (1011)
library_books

Genomic evidence for intraspecific hybridization in a clonal and extremely halotolerant yeast

2018
BMC Genomics
PMCID: 5952469
PMID: 29764372
DOI: 10.1186/s12864-018-4751-5

[…] ed Nucleic Acid Parser (SNAP) [] was bootstrap-trained within MAKER based on the gene models derived from the alignment of the protein datasets to the genome as recommended by Campbell et al. (2014). GeneMark-ES (Lomsadze et al., 2014) was self-trained [] and Augustus was used with the training parameters for Neurospora crassa [].The genome assembly and gene prediction completeness was evaluated w […]

library_books

Complete Genome Sequences of Bacillus Phages Janet and OTooleKemple52

2018
Genome Announc
PMCID: 5946042
PMID: 29748396
DOI: 10.1128/genomeA.00083-18

[…] resulting in ∼100-fold depth of coverage. Gene annotation was completed using DNA Master (see http://cobamide2.bio.pitt.edu/computer.htm), which includes the open reading frame (ORF) prediction tools GeneMark () and Glimmer () and the tRNA prediction tool ARAGORN (). Functional analysis was performed using BLASTp () and HHpred ().Janet has a length of 160,705 bp, with terminal repeats of 2,434 bp, […]

library_books

Whole genome and transcriptome analysis reveal adaptive strategies and pathogenesis of Calonectria pseudoreteaudii to Eucalyptus

2018
BMC Genomics
PMCID: 5946483
PMID: 29747580
DOI: 10.1186/s12864-018-4739-1

[…] Gene structure was predicted using the PASA pipeline with a combination of ab-initio and RNA-Seq evidence based approaches []. For ab-initio predictions, Augustus, SNAP, Transdecoder and GeneMark-ES v2 were employed to predict coding genes [–]. The EVidenceModeler (EVM) was used to compute weighted consensus gene annotations based on ab-initio gene models and transcript evidence deriv […]

library_books

Analysis of Theileria orientalis draft genome sequences reveals potential species level divergence of the Ikeda, Chitose and Buffeli genotypes

2018
BMC Genomics
PMCID: 5921998
PMID: 29703152
DOI: 10.1186/s12864-018-4701-2

[…] train genome assemblies were masked using RepeatMasker v4.0.7. With repeat masked sequences, ab initio annotation tracks were derived from gene predictors Augustus v3.2.3 [], Snap v2013–11-29 [], and GeneMark ES Suite v4.32 [] utilizing both GeneMark ET (Robertson and Fish Creek), and GeneMark ES (Goon Nure). A training set based on EST alignments (RNA data sourced from the Shintoku WGS project [] […]

library_books

De Novo DNA Synthesis in Aedes aegypti Midgut Cells as a Complementary Strategy to Limit Dengue Viral Replication

2018
Front Microbiol
PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] architecture is shown in Supplementary Figure .An exon prediction analysis was made using five different tools: Augustus (Keller et al., ), FGenesh (Salamov and Solovyev, ), GeneID (Blanco et al., ), GeneMark (Besemer and Borodovsky, ) and GenScan (Burge and Karlin, ). Hnt CDS and mRNA coding regions were deduced and oligonucleotide primers for hnt amplification were designed, sequences in Supplem […]

library_books

The Phytophthora cactorum genome provides insights into the adaptation to host defense compounds and fungicides

2018
Sci Rep
PMCID: 5916904
PMID: 29695739
DOI: 10.1038/s41598-018-24939-2

[…] n-coding genes in the genome. First, the genome was repeat masked using the result of repeat annotation. Then the masked genome was fed to the MAKER2 pipeline with the ab initio gene predictors being GeneMark-ES, FGENESH, Augustus and SNAP. And for the evidence-driven gene prediction, cDNA of P. infestans and proteins of six related species from Ensembl (release-28, P. infestans, P. kernoviae, P. […]

Citations

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GeneMark institution(s)
School of Biology, Georgia Institute of Technology, Atlanta, GA, USA; Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA

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