GeneMarkS statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GeneMarkS

Tool usage distribution map

This map represents all the scientific publications referring to GeneMarkS per scientific context
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Associated diseases

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GeneMarkS specifications


Unique identifier OMICS_29661
Name GeneMarkS
Alternative name GeneMarkS-2
Interface Web user interface
Restrictions to use None
Input data A sequence.
Input format FASTA, multiFASTA
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Mark Borodovsky
  • person_outline Alex Lomsadze

Additional information

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Publications for GeneMarkS

GeneMarkS citations


Identification and pathogenomic analysis of an Escherichia coli strain producing a novel Shiga toxin 2 subtype

Sci Rep
PMCID: 5928088
PMID: 29712985
DOI: 10.1038/s41598-018-25233-x
call_split See protocol

[…] cBio) sequencing platform. The data were assembled to generate one circular genome without gaps by using SMRT Analysis 2.3.0. The protein-coding sequences (CDSs), tRNAs and rRNAs were predicted using GeneMarkS. The prophages were predicated by the PHAge Search Tool (PHAST). The virulence factors were predicted through the BLAST tool of NCBI and by using the virulence factor database (VFDB; http:// […]


Comparative mitochondrial genomics of cryptophyte algae: gene shuffling and dynamic mobile genetic elements

BMC Genomics
PMCID: 5910586
PMID: 29678149
DOI: 10.1186/s12864-018-4626-9
call_split See protocol

[…] d.Protein coding genes as well as rRNA and tRNA genes were compiled from all previously sequenced cryptophyte mitochondrial genomes. Preliminary annotation of protein coding genes was performed using GeneMarkS ( The final annotation file was checked in Geneious Pro 10.2.2 ( using the ORFfinder with genetic code 4 (Protozoan Mitocho […]


Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome

Virol J
PMCID: 5891951
PMID: 29636072
DOI: 10.1186/s12985-018-0976-9

[…] 000000.1).Then, this marine metagenome for which the annotation was performed by automatic pipeline, was further investigated. Amongst 111 contigs, all genes and proteins were predicted de novo using GenemarkS [], with a blastp analysis of the 1947 predicted proteins followed by GC% assignment of putative viral contigs (Additional files  and ). Indeed, we used an e-value cut-off at 10− 2 and our r […]


Genome Wide Analysis of Mycoplasma bovirhinis GS01 Reveals Potential Virulence Factors and Phylogenetic Relationships

PMCID: 5940136
PMID: 29602809
DOI: 10.1534/g3.118.200018

[…] as generated. The depth of coverage distribution map for genome assembly is shown in Figure S2 in File S1.The genome component prediction was conducted as follows: gene prediction was conducted using GeneMarkS v4.17 () with default parameters. Transfer RNAs (tRNAs) were identified using tRNAscan-SE v1.3.1 () with default parameters. Ribosomal RNAs (rRNAs) were detected using RNAmmer v1.2 () with d […]


Next Generation Sequencing of Haematococcus lacustris Reveals an Extremely Large 1.35 Megabase Chloroplast Genome

Genome Announc
PMCID: 5864939
PMID: 29567741
DOI: 10.1128/genomeA.00181-18
call_split See protocol

[…] chical Genome Assembly Process (HGAP) version 2 algorithm (), yielding a single contig. Over 91,000 subreads, with a mean subread length of 8,900 bp, went into the assembly of the chloroplast genome. GeneMarkS version 4.17 () was used to generate gene predictions ab initio. Gene annotations were generated through the Synthetic Genomics, Inc. (La Jolla, CA, USA) proprietary Archetype annotation pip […]


Identification and Characterization of Mycemycin Biosynthetic Gene Clusters in Streptomyces olivaceus FXJ8.012 and Streptomyces sp. FXJ1.235

Mar Drugs
PMCID: 5867642
PMID: 29558441
DOI: 10.3390/md16030098
call_split See protocol

[…] Hiseq system (Novogene, Beijing, China), resulting in a total of 8,852,829 bp of genome sequence distributed across 48 contigs (≥600 bp). The sequences obtained were annotated using Glimmer 3.02 [], GeneMarkS [], and BlastP []. The DNA sequences of mycemycin gene clusters have been deposited in the GenBank database. The accession number for mym is MG837055 and the numbers for mye are MG837053 (pa […]

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GeneMarkS institution(s)
Wallace H. Coulter Department of Biomedical Engineering, Atlanta, GA, USA; School of Computational Science and Engineering, Atlanta, GA, USA; School of Biological Sciences, Georgia Tech, Atlanta, GA, USA; Gene Probe, Inc., Atlanta, GA, USA; Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, Moscow, Russia
GeneMarkS funding source(s)
Supported by National Institutes of Health (NIH) [HG000783].

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