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EasyGene specifications

Information


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

Maintainer


  • person_outline Pernille Nielsen

Publications for EasyGene

EasyGene citations

 (43)
library_books

Identification of new protein coding genes with a potential role in the virulence of the plant pathogen Xanthomonas euvesicatoria

2017
BMC Genomics
PMCID: 5559785
PMID: 28814272
DOI: 10.1186/s12864-017-4041-7

[…] nnotation 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 softwar […]

library_books

Genomic and transcriptomic analyses reveal distinct biological functions for cold shock proteins (VpaCspA and VpaCspD) in Vibrio parahaemolyticus CHN25 during low temperature survival

2017
BMC Genomics
PMCID: 5460551
PMID: 28583064
DOI: 10.1186/s12864-017-3784-5

[…] imer 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, GenBa […]

library_books

Draft Genome Sequence of the Plant Growth Promoting Rhizobacterium Pseudomonas fluorescens Strain CREA C16 Isolated from Pea (Pisum sativum L.) Rhizosphere

2017
Genome Announc
PMCID: 5270692
PMID: 28126933
DOI: 10.1128/genomeA.01456-16

[…] age 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 […]

library_books

Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism induced responses in the early exponential growth phase

2016
BMC Genomics
PMCID: 4972977
PMID: 27487841
DOI: 10.1186/s12864-016-2840-x

[…] R and 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 system […]

library_books

Genetic characterization of ØVC8 lytic phage for Vibrio cholerae O1

2016
Virol J
PMCID: 4802629
PMID: 27000701
DOI: 10.1186/s12985-016-0490-x

[…] to 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 the molecula […]

library_books

A Novel Quality Measure and Correction Procedure for the Annotation of Microbial Translation Initiation Sites

2015
PLoS One
PMCID: 4512697
PMID: 26204119
DOI: 10.1371/journal.pone.0133691

[…] teria, where the reported number varies between 9.2% and 88.4% [,].Currently the most widely used gene-calling tools are GLIMMER3 [] and Prodigal []. Other tools include MED2.0 [], GeneMarkHmm [] and EasyGene []. The former tools predict coding sequences with relative low error rates for genomes of well-studied organisms. Nevertheless, the annotation of genes in high-GC-content genomes using these […]

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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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