Circoletto protocols

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Circoletto statistics

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Circoletto specifications

Information


Unique identifier OMICS_07484
Name Circoletto
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
License MIT License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Nikos Darzentas <>
  • person_outline Circoletto Team <>

Information


Unique identifier OMICS_07484
Name Circoletto
Interface Web user interface
Restrictions to use None
Input data Either two nucleotide or amino acid sequence files, the query and database or a precomputed pairwise alignment BLAST output.
Input format FASTA, TXT
Output data Sequences placed around a circle, read clockwise, starting at 12 o’clock.
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainers


  • person_outline Nikos Darzentas <>
  • person_outline Circoletto Team <>

Publication for Circoletto

Circoletto in pipelines

 (3)
2017
PMCID: 5282782
PMID: 28163827
DOI: 10.1186/s40793-017-0227-5

[…] belgium) was utilized for the visualization of synteny among the crispr regions of aca-dc 2 and lmd-9 strains. the edgar server [] was used for whole genome phylogeny and venn diagram analysis. circoletto [] was employed for whole genome alignment among s. thermophilus strains. finally, the genomic islands were identified through the islandviewer 3 web-based resource []., the complete […]

2017
PMCID: 5589831
PMID: 28883533
DOI: 10.1038/s41598-017-11495-4

[…] per site per year, we calculated the divergence time (t) as t = ks/(2 × 6.1 × 10 − 9) × 10 − 6 mya. next, to identify syntenic regions within each soybean cwrd related gene family, we used circoletto (http://tools.bat.infspire.org/circoletto/)., genomic sequences of 505 soybean cwrd related gene members were subjected to identification of ssrs in microsatellite identification tool […]

2017
PMCID: 5655121
PMID: 29104571
DOI: 10.3389/fmicb.2017.02054

[…] (finn et al., ). a multiple amino acid sequence alignment of the ph-4 candidates and ph-4 homologs in genbank was performed using clustalw (thompson et al., ), and the alignment was visualized using circoletto with an e-value ≤ 1 e−5 (darzentas, ). an unrooted phylogenetic tree was also constructed using mega6 based on the maximum likelihood algorithm (tamura et al., ), and the tree topology […]


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Circoletto in publications

 (22)
PMCID: 5921756
PMID: 29703137
DOI: 10.1186/s12864-018-4695-9

[…] the gsds software (http://gsds.cbi.pku.edu.cn/; [])., duplication analysis for caarf genes was performed using plant genome duplication database (pgdd; http://chibba.agtec.uga.edu/duplication/; []). circoletto tool was used to determine and plot sequence similarity []. to define a tandem cluster, the following parameters were established: a cluster should contain at least two genes; a sliding […]

PMCID: 5845707
PMID: 29559980
DOI: 10.3389/fimmu.2018.00448

[…] was based on the algorithm described by boyd et al. (). clonal type definition was based on v and j gene usage and cdr3-region at the nucleotide level. rearrangements were visualized using circoletto plots [www.circos.ca ()]. cdr3 amino acid compositions were visualized using weblogo online tool [www.weblogo.berkeley.edu (, )]., the ngs trg-trd data set has been submitted […]

PMCID: 5789830
PMID: 29382843
DOI: 10.1038/s41598-018-19535-3

[…] tpck (chromosome of translocation proto-calepineae karyotype, ancestral genome of brassica species), block (a, b, c, etc), lf, mf1, mf2, and gene ids. graphical representation was achieved using the circoletto webtool (http://tools.bat.infspire.org/circoletto/) by providing the fasta sequences in each block for all three brassica species and arabidopsis., the exon/intron organization […]

PMCID: 5660997
PMID: 29118750
DOI: 10.3389/fmicb.2017.02097

[…] rna secondary prediction was performed with the mfold web server http://unafold.rna.albany.edu/?q=mfold/rna-folding-form. eventually, sequence similarity levels were visualized using the circoletto tool with standard parameters http://tools.bat.infspire.org/circoletto/ potential panhandle structures derived from partially complementary virus sequence termini were assessed […]

PMCID: 5589831
PMID: 28883533
DOI: 10.1038/s41598-017-11495-4

[…] per site per year, we calculated the divergence time (t) as t = ks/(2 × 6.1 × 10 − 9) × 10 − 6 mya. next, to identify syntenic regions within each soybean cwrd related gene family, we used circoletto (http://tools.bat.infspire.org/circoletto/)., genomic sequences of 505 soybean cwrd related gene members were subjected to identification of ssrs in microsatellite identification tool […]


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Circoletto institution(s)
Institute of Agrobiotechnology, Centre for Research and Technology Hellas, Thessaloniki, Greece

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