ACT protocols

ACT specifications

Information


Unique identifier OMICS_00928
Name ACT
Alternative name Artemis Comparison Tool
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format EMBL, GENBANK, GFF, FASTA, raw
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Tim Carver <>

Information


Unique identifier OMICS_00928
Name ACT
Alternative name Artemis Comparison Tool
Interface Web user interface
Restrictions to use None
Input format EMBL, GENBANK, GFF, FASTA, raw
Programming languages Java
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Tim Carver <>

Publications for Artemis Comparison Tool

ACT IN pipelines

 (31)
2018
PMCID: 5863386
PMID: 29562943
DOI: 10.1186/s40168-018-0440-5

[…] at genomic level., at the nucleotide level, pairwise genome alignment of the two strains of lactobacillus spp. was generated with webact (blastn with default parameters) [73] and visualized with the artemis comparison tool (act, score cutoff with 2000) [74]. for the analysis, the replication origin of each genome was located with the web-based system ori-finder [75]. strain-specific genes […]

2017
PMCID: 5282893
PMID: 28163825
DOI: 10.1186/s40793-017-0234-6

[…] differences between the coding regions of the genomes. structural analyses were conducted by comparing the four genomes with a local database using blastn, and the results were analyzed using the artemis comparison tool [21]. the mb11 and mb14 strains showed extensive structural similarity, while mb30 had a large inversion of approximately 1.2 mbp compared to mb14 (fig. 5). however, mb66 […]

2017
PMCID: 5371807
PMID: 28335474
DOI: 10.3390/v9030052

[…] prior to analysis, the gaps between the assembled annotated contigs of each draft genome were made the same length by adding a known length of ambiguous nucleotides (i.e., a series of 10 ns). the artemis comparison tool (act) was then used for blastn pairwise alignment and visualization of the draft genome sequences against the fully assembled non-gapped reference genome of ehv-86 [59]. […]

2017
PMCID: 5640839
PMID: 28814514
DOI: 10.1128/JVI.01058-17

[…] tool (71) was used for scaffolding the contigs. the assembled genome was compared with that of the asfv parental virulent ba71 strain (genbank accession number kp055815.1) (46) using artemis comparison tool (72), and gepard software 1.4v was used to calculate dot plots for genome comparisons (73). the ba71 sequence (genbank accession number kp055815.1) was also used […]

2016
PMCID: 4759546
PMID: 26891997
DOI: 10.1038/srep21399

[…] concatenation of contigs of maff 212056 was performed to generate a virtual single genome sequence. then, a draft genome of maff 212056 was compared with the biovar 1 genome (icmp 9617) using the artemis comparison tool (act) (http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act)20., toxin synthesis genes and type iii secreted effector (t3se) genes were considered […]

ACT institution(s)
Wellcome Trust Sanger Institute Wellcome Trust Genome Campus, Hinxton, Cambridge, UK

ACT review

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Ben Huang

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Desktop
The program sound great, but it is hard to know where to start. At the end, it is useless!