Easyfig protocols

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Easyfig specifications

Information


Unique identifier OMICS_00907
Name Easyfig
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input format Genbank, EMBL, FASTA
Output format BMP, SVG
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche, Oxford Nanopore
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.1
Stability Stable
Requirements
Tkinter library
Maintained Yes

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  • person_outline mjsull <>

Publication for Easyfig

Easyfig in pipelines

 (23)
2018
PMCID: 5767256
PMID: 29375524
DOI: 10.3389/fmicb.2017.02659

[…] 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 encoded by phages was conducted by easyfig software (). orfs were searched by blast in virulence factor database (vfdb) and antibiotic resistance gene database (ardb), to ensure its safety in vivo. the whole genome of phage sh-ab15519 […]

2018
PMCID: 5795452
PMID: 29337868
DOI: 10.3390/v10010039

[…] determination obtained by sanger sequencing (eurofins mwg operon, les ullis, france). structural and functional annotations were obtained from prokka []. genome alignments were performed using easyfig []. complete sequences of the salmonella bacteriophage prd1 and bacillus phage bam35c (genbank accession numbers: nc_001421 and prjna14311, respectively) were used for comparison. […]

2018
PMCID: 5816814
PMID: 29487585
DOI: 10.3389/fmicb.2018.00202

[…] table ). determination of sequence homologies and the identification of snps were conducted by using the blast tools available at the ncbi website. genome alignments were visualized with easyfig (sullivan et al., ) and modified using inkscape. the left and right repeats were defined using a pile-up analysis of raw sequencing reads after mapping with clc workbench 9.0 (qiagen, hilden, […]

2018
PMCID: 5893538
PMID: 29636463
DOI: 10.1038/s41426-018-0065-6

[…] genomic structures are associated with the insertion site of the csep1 gene, the flanking genes of csep1-negative and positive c. concisus strains were compared using blastn and visualised using easyfig,., the phylogenetic tree of the 26 csep1 genes from the 63 oral c. concisus strains was generated using the maximum likelihood method implemented in mega6., c. concisus p2cdo4, which contains […]

2017
PMCID: 5261728
PMID: 28118395
DOI: 10.1371/journal.pone.0170734

[…] (kt 630646), sen22 (kt 630648), and sen34 (kt 630649). genomes of salmonella phages were analyzed using the lasergene program package (dnastar). blast comparisons of phage genomes were produced with easyfig []. average nucleotide identity (ani) of phages was calculated by the jsspeciesweb server running mummer 3.0 software [, ]., phage samples for electron microscopy were prepared from phage […]


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Easyfig in publications

 (144)
PMCID: 5958079
PMID: 29773850
DOI: 10.1038/s41598-018-26180-3

[…] replicon sequences were submitted to genbank and registered under bioproject id prjeb22129., sequence alignment and graphic comparison were performed using the genome comparison visualizer easyfig., in order to confirm bioinformatics function assignment, experimental functional analysis was carried out for putative origins of replication, including replication initiation proteins […]

PMCID: 5945888
PMID: 29780362
DOI: 10.3389/fmicb.2018.00793

[…] sequences was carried out by emboss needle tool at embl-ebi (european molecular biology laboratory-european bioinformatics institute). comparison of orfs from relative phages was performed using easyfig (http://mjsull.github.io/easyfig/files.html) (sullivan et al., ). phylogenetic analyses between the genomes of related phages were performed with mega using the neighbor-joining algorithm., […]

PMCID: 5918551
PMID: 29713466
DOI: 10.1186/s13756-018-0349-6

[…] annotate the genomes of the plasmid. the circular map of the pec463-ndm5 plasmid was generated using the cgview server []. a comparison of pec463-ndm5 and three related plasmids was performed with easyfig 2.2.2 []. the rested plasmid sequences were mapped to the representative plasmid sequence with clc genomics workbench version 8.0., incompatibility typing of the blandm plasmid was performed […]

PMCID: 5880901
PMID: 29636744
DOI: 10.3389/fmicb.2018.00577

[…] checked by sequence alignment against the online server sequence similarity search – blast. pairwise comparisons of specific genomic clusters within l. ferriphilum strains were visualized using easyfig v2.1 (). in addition, rrna and trna genes were predicted using the online servers rnammer v1.2 () and trnascan-se v2.0 (), respectively., the data sets for draft genomes of l. ferriphilum dx […]

PMCID: 5854631
PMID: 29545614
DOI: 10.1038/s41598-018-22883-9

[…] orthologs of genes rv2044c-pnca-rv2042c as well as to identify whether the deletion in rv2044c was present in other members of the mtbc and m. canettii. as shown in fig.  (a comparison made using easyfig), these genes are highly conserved among various lineages of mtbc and m. canettii, but the lineage 3 specific frameshift deletion in rv2044c was not identified in representative isolates […]


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Easyfig institution(s)
University of Queensland, Queensland, Australia

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