EasyGene protocols

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EasyGene specifications


Unique identifier OMICS_16681
Name EasyGene
Interface Web user interface
Restrictions to use None
Input data A genome sequence.
Output data A list of statistically significant genes.
Computer skills Basic
Version 1.2
Stability Stable
Maintained Yes


  • person_outline Pernille Nielsen <>

Publications for EasyGene

EasyGene in pipelines

PMCID: 3877037
PMID: 24391756
DOI: 10.1371/journal.pone.0083346

[…] described in detail in this study were manually annotated using blastx with standard parameters and pfam domain search (version 27.0.) . open reading frames (orfs) were predicted using the easygene server , . a genetic map of plasmid pcadab1 was generated using dnaplotter . copy numbers of genetic elements was estimated by comparing sequence coverages, as seen elsewhere ., […]

PMCID: 2974192
PMID: 20623278
DOI: 10.1007/s00248-010-9717-3

[…] of the outcome., the predicted proteomes comprising all protein-coding genes were extracted from the genbank files for the published genomes. for unpublished genomes, they were predicted using easygene []. all predicted proteomes were compared by blastp reciprocal pairwise comparison. two genes were attributed to a single gene family and considered 'conserved' when they shared at least 50% […]

PMCID: 2807590
PMID: 19830476
DOI: 10.1007/s00248-009-9596-7

[…] as more genomes are added, whilst the core genome representing conserved gene families slowly decreases with the addition of more genomes., the predicted genes of every genome (annotated or found by easygene) were translated and every gene was compared, by blastp against every other genome and its own genome. in the latter case, the hit to self was ignored. the 50/50 rule for blast hits […]

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EasyGene in publications

PMCID: 5559785
PMID: 28814272
DOI: 10.1186/s12864-017-4041-7

[…] of as many genes as possible, the basis for detailed functional analyses. coding sequences (cds) are usually annotated using gene prediction software such as glimmer, prodigal, genemark and easygene [–]. the high coding capacity (up to 90%) of bacterial, viral and archaeal genomes [] require a high accuracy of gene prediction programs. an important quality parameter of prediction […]

PMCID: 5460551
PMID: 28583064
DOI: 10.1186/s12864-017-3784-5

[…] walking and combinatorial pcr as previously described []. the final genome assembly was performed using the phred-phrap-consed software packages []. protein-coding genes were predicted using the easygene software [], and functional assignments were inferred based on standalone basic local alignment search tool (blast) ( http://www.ncbi.nlm.nih.gov/blast) searches against the swiss-prot, […]

PMCID: 5270692
PMID: 28126933
DOI: 10.1128/genomeA.01456-16

[…] tool from the bedtools package (). the mean and median coverage depths were 23.24× and 26×, respectively., reference-based gene identification was performed running the prokaryotic gene finder tool easygene () using pseudomonas aeruginosa pao1 as reference, the prodigal gene-finding algorithm (), and the fgenesb (softberry) using the “archae bacterial generic” as the closest organism. the final […]

PMCID: 4972977
PMID: 27487841
DOI: 10.1186/s12864-016-2840-x

[…] sequencing of the product or direct sequencing on selected fosmids., genome annotation was done analogously as in our previous study []. briefly, coding dna sequences (cdss) were determined using easygene [] and prodigal [], and gene functions were assigned using rast [] and pannzer []. the crisprfinder [], bagel2 [], cw-pred [], and phast [] programs were utilized to predict crispr/cas […]

PMCID: 4802629
PMID: 27000701
DOI: 10.1186/s12985-016-0490-x

[…] compare the øvc8 genome sequence against the sequences of proteins reported in the databases. open reading frames (orfs) identified using the glimmer3, meta geneannotator, genemarks, zcurve_v, and easygene gene prediction programs were grouped as a single locus. trnas and rrnas were predicted using the trnascan-se, rfam, and arnmmer programs. the pi/mw program was used to calculate […]

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EasyGene institution(s)
Bioinformatics Centre, Institute of Molecular Biology and Physiology, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark

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