Artemis protocols

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Associated diseases

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Artemis specifications

Information


Unique identifier OMICS_00903
Name Artemis
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Javascript, Shell (Bash)
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Medium
Version 17.0.1
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Tim Carver <>

Additional information


http://sanger-pathogens.github.io/Artemis/

Publication for Artemis

Artemis in pipelines

 (30)
2018
PMCID: 5906601
PMID: 29670192
DOI: 10.1038/s41598-018-24382-3

[…] the prediction of protein-coding genes, rrnas and trnas was done using mitos and arwen software and validated manually by comparing homologous regions with a loa loa mitochondria reference in artemis. a mitogenome map was generated using the brig software package., a provisional mitogenome nucleotide sequence assembly was aligned to a set of 21 previously published nematode mitogenome […]

2018
PMCID: 5923468
PMID: 29614052
DOI: 10.3390/v10040174

[…] using the sequence logo generator (weblogo) []. the host rnap promoters were identified using bprom []. all the identified promoter and terminator sequences were further verified manually using the artemis. the phylogenetic trees for the amino acid sequences of the dna ligase, rnap, and capsid proteins were constructed using the service at phylogeny.fr []. the phylogenetic tree of the whole […]

2017
PMCID: 5268413
PMID: 28125655
DOI: 10.1371/journal.pone.0170676

[…] pseudotuberculosis isolated over 16 years (1996–2012)., the nucleotide sequences of ris for the seven sequenced genomes and other five genomes of bacteria isolated in california were recovered with artemis software and analyzed using fragmented all-against-all comparison with the gegenees software v. 2.2.1 []. the comparative results of gegenees are presented as a heatmap containing […]

2017
PMCID: 5268413
PMID: 28125655
DOI: 10.1371/journal.pone.0170676

[…] with an optical map., the number of trnas was determined with the tool trnascan-se []. the numbers of cdss, rrna clusters, pseudogenes, and contigs were manually specified using the software artemis v.14.0.0 []. the access numbers for each strain are: c. pseudotuberculosis mb44 (mcoc01000000), c. pseudotuberculosis mb122 (mcob01000000), c. pseudotuberculosis mb154 (mcoa01000000), c. […]

2017
PMCID: 5399257
PMID: 28428298
DOI: 10.1128/genomeA.00193-17

[…] reading frames within the draft genome, and the rast annotation server () was used to determine complementary gene calling and automated annotation. the draft genome was manually analyzed using the artemis genome browser (), and comparative analysis with the genome of s. saprophyticus atcc 15305 () was performed using the artemis comparison tool (act) (). the phast (phage search tool) web […]


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Artemis in publications

 (78)
PMCID: 5936940
PMID: 29765675
DOI: 10.1098/rsos.172212

[…] using an illumina genome analyzer ii [] yielding 26 007 384 76 bp paired-end reads with a median insert size of 244.1 bp (erx005631). protein sequences were retrieved from the embl files using artemis []. two l. panamensis genomes, two l. peruviana genome assemblies and five 100 bp paired-end illumina hiseq 2000 read libraries of other viannia isolates [] were used for comparison (). […]

PMCID: 5902956
PMID: 29661152
DOI: 10.1186/s12866-018-1179-7

[…] option. all genome assemblies were evaluated using the quast tool []. protein coding sequences (cdss) were predicted using metagenemark []. the sdr-gene sequences were manually isolated using artemis []., mlst analysis was carried out for the representative s. aureus isolates. nucleotide sequences of the following house keeping genes: arcc (carbamate kinase), aroe (shikimate […]

PMCID: 5896035
PMID: 29682169
DOI: 10.1186/s40793-018-0310-6

[…] greater than 80 amino acids. if alignment lengths were smaller than 80 amino acids, we used an e-value of 1e-05. such parameter thresholds have already been used in previous works to define orfans. artemis [] was used for data management, and dna plotter [] was used for visualization of genomic features. the mauve alignment tool was used for multiple genomic sequence alignment []. to identify […]

PMCID: 5923468
PMID: 29614052
DOI: 10.3390/v10040174

[…] genome sequences were aligned using the multiple sequence alignment program mafft [] at the chipster platform []. the annotations were performed using rast server [] and manually annotated using the artemis genome browser and annotation tool []. some rast-identified open reading frames (orfs) missed a good ribosomal binding site (rbs) and were corrected to a start codon with an appropriately […]

PMCID: 5835047
PMID: 29535698
DOI: 10.3389/fmicb.2018.00333

[…] tool version 0.95 (alikhan et al., ). all genomes were tried as reference in brig analysis, to extract out most significant atypical regions. observed atypical genomic regions were taken out by artemis comparisons (carver et al., ). pangenome analysis was carried for all 49 genomes, out by bpga v1.3 (chaudhari et al., ). a minimum identity of 50% was used as the cut-off. number […]


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Artemis institution(s)
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
Artemis funding source(s)
Supported by the Wellcome Trust through their funding of the Pathogen Genomics group at the Wellcome Trust Sanger Institute (grant number WT 076964).

Artemis review

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Pablo Smircich

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Desktop
The Artemis genome browser is also a feature rich annotation tool. I use it frequently when I need to view my own tracks, either annotation or quantitative information.
One of the best and I think a little bit hidden feature is that you can create a configuration file with many options to change the default UI when the software initiates.