GeneMark protocols

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GeneMark specifications


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


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  • person_outline Mark Borodovsky <>
  • person_outline Alex Lomsadze <>

Publication for GeneMark

GeneMark in pipelines

PMCID: 5698912
PMID: 29188023
DOI: 10.5256/f1000research.13945.r27739

[…] et al. ( ). this suggests our two australian isolate assemblies are as complete references as those currently available., we conducted a preliminary protein-coding sequence prediction using genemark-es v4.32 , which utilises a self-training algorithm to identify exon, intron and intergenic regions as well as initiation and termination sites. genemark-es was run using the default […]

PMCID: 5754475
PMID: 29301895
DOI: 10.1128/genomeA.00839-17

[…] checked for quality and adapter contamination using trim galore () and then assembled into contigs using a spades genome assembler (). dna ends were conformed via pcr. genes were predicted using genemark () and were manually annotated using the ncbi protein nr database. the family of phage tyrion was predicted using virfam analysis (). electron microscopy was carried out at socolofsky […]

PMCID: 5764923
PMID: 29326199
DOI: 10.1128/genomeA.01101-17

[…] has diverged considerably from subcluster p1 phages, the p1 phages have extensive sequence similarity to cluster i phages in this region (). genomes were auto-annotated using glimmer () and genemark () and refined by manual inspection; the number of protein-coding genes ranges from 76 to 81 (). functions were assigned using phamerator (), blastp (), and hhpred (). no trnas are present […]

PMCID: 5767256
PMID: 29375524
DOI: 10.3389/fmicb.2017.02659

[…] a total of 29,226,076 trimmed reads were obtained. the sequence assembly and optimization procedures were conducted by soapdenovo2 software (). possible open reading frames (orfs) were predicted by genemark software (). functional annotation of orfs and homology assignments between genes from phage sh-ab 15519 and other phages were performed by the blastp. alignment of functional proteins […]

PMCID: 5773145
PMID: 29343217
DOI: 10.1186/s12864-018-4440-4

[…] were used in this work to improve gene prediction. mapping these reads into the assembled genome using star [] produced splicing junction information, which were used in the self-training step of genemark-es [] for the first prediction round. we used the braker1 pipeline [] with the splicing junctions’ information and the predictions from genemark-es to create a list of reliable genes. next, […]

GeneMark in publications

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

[…] 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 […]

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

[…] v4-0-3., 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 […]

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

[…] in ∼100-fold depth of coverage. gene annotation was completed using dna master (see, 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 […]

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

[…] 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 […]

PMCID: 5932203
PMID: 29755433
DOI: 10.3389/fmicb.2018.00801

[…] reverse translation allowed us to find the genome coordinates of hnt. the complete genomic region was screened for coding-sequences (cds) using mrna prediction tools like augustus, fgenesh, geneid, genemark, and genscan (burge and karlin, ; salamov and solovyev, ; besemer and borodovsky, ; blanco et al., ; keller et al., )., the sequences of hnt and mammal orthologue ras responding binding […]

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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