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CCT specifications

Information


Unique identifier OMICS_19852
Name CCT
Alternative name CGView Comparison Tool
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl, Shell (Bash)
Computer skills Advanced
Stability Stable
Requirements
Blast, Java, ImageMagick, BioPerl
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Paul Stothard
  • person_outline Jason Grant
  • person_outline Adriano Arantes

Additional information


http://stothard.afns.ualberta.ca/downloads/CCT/creating_maps.html http://stothard.afns.ualberta.ca/downloads/CCT/commands.html http://stothard.afns.ualberta.ca/downloads/CCT/installation.html Tuto: http://stothard.afns.ualberta.ca/downloads/CCT/tutorials.html

Publication for CGView Comparison Tool

CCT citations

 (32)
library_books

Comparative genomics of cocci shaped Sporosarcina strains with diverse spatial isolation

2018
BMC Genomics
PMCID: 5930826
PMID: 29716534
DOI: 10.1186/s12864-018-4635-8

[…] entity between each of the 29 cocci-shaped Sporosarcina genomes, a BLAST Atlas comparing all the genomes to each strain as the reference genome were generated using the montage project command in the CGView Comparison Tool []. To visualize the results, strains with complete genomes were utilized as the reference genomes. The visualized reference strains included S204 that is closely related to the […]

library_books

Physiological and Comparative Genomic Analysis of Arthrobacter sp. SRS W 1 2016 Provides Insights on Niche Adaptation for Survival in Uraniferous Soils

2018
Genes
PMCID: 5793183
PMID: 29324691
DOI: 10.3390/genes9010031

[…] t [] with the layout specified. Contigs were then reordered and reversed as needed to match the ordering determined by mummerplot.A circular genomic map of strain SRS-1-W-2016 was generated using the CGView Comparison Tool []. Island Viewer was used to identify chromosomal deviations in GC content, known as genomic islands (GEIs) (http://www.pathogenomics.sfu.ca/islandviewer/) []. The genome, with […]

library_books

Pacbio sequencing of copper tolerant Xanthomonas citri reveals presence of a chimeric plasmid structure and provides insights into reassortment and shuffling of transcription activator like effectors among X. citri strains

2018
BMC Genomics
PMCID: 5755412
PMID: 29301493
DOI: 10.1186/s12864-017-4408-9

[…] , differed remarkably in the plasmid copy number as well as TALE composition (Table ). We compared plasmid P2 of Xc-03-1638-1-1 to the three plasmids of LM180, pLM180.2, pLM180.3, and pLM180.4, using CGView comparison tool [] (Fig. ). Plasmid pLM180.2, (64 kb in size) contains one intact TALE with 13.5 repeats (belonging to pthA2/3 subgroup, Additional file : Table S1). Plasmid pLM180.3 and pLM180 […]

library_books

Comparative Analysis of 37 Acinetobacter Bacteriophages

2017
Viruses
PMCID: 5795418
PMID: 29295549
DOI: 10.3390/v10010005

[…] d gene product content between the Acinetobacter phages and the wider sequenced phage pool were performed using CoreGenes3.5 []. Genome maps were prepared in Scalable Vector Graphics format using the CGView Comparison Tool [] or EasyFig [] and edited using Adobe Illustrator.Phage transmission electron micrographs were provided courtesy of members of the phage research community (c.f. Acknowledgeme […]

library_books

Genomic analysis of endemic clones of toxigenic and non toxigenic Corynebacterium diphtheriae in Belarus during and after the major epidemic in 1990s

2017
BMC Genomics
PMCID: 5683216
PMID: 29132312
DOI: 10.1186/s12864-017-4276-3

[…] e genes including sapA (DIP2066), adhesin of Sdr family (DIP2093) and BigA-like adhesin (CDC7B_1983; DIP2014) were searched within the dataset using EDGAR. The CDS BLAST maps were generated using the CGView Comparison Tool [] for isolates in ST5 and ST8 using concatenated sequence of ISS 4060 and NCTC 13129 as the reference, respectively. MLST profiles were extracted from the genome sequences usin […]

library_books

Shared features of cryptic plasmids from environmental and pathogenic Francisella species

2017
PLoS One
PMCID: 5570271
PMID: 28837612
DOI: 10.1371/journal.pone.0183554

[…] each plasmid were drawn using the CGView software [], and additional labels (ori, ter, Rep, repeats, DnaA boxes, restriction site locations) were added to the maps manually. Additionally, the program CGView Comparison Tool [] was used to compare groups of plasmids for coding sequence similarity.Rep protein sequences were aligned by MUSCLE [] within MEGA 7.0 [], using default parameters. Maximum li […]

Citations

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CCT institution(s)
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AL, Canada; Bioinformatics Laboratory, National Microbiology Laboratory, University of Manitoba, Winnipeg, MB, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, Canada

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