Circoletto statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Circoletto
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Tool usage distribution map

This map represents all the scientific publications referring to Circoletto per scientific context
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Associated diseases

This word cloud represents Circoletto usage per disease context
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Popular tool citations

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Protocols

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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Versioning


No version available

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 citations

 (18)
library_books

Genome wide identification of the auxin response factor gene family in Cicer arietinum

2018
BMC Genomics
PMCID: 5921756
PMID: 29703137
DOI: 10.1186/s12864-018-4695-9

[…] LE and MEGA, respectively. Exon-intron distributions were analyzed using GSDS server. Gene duplications were determined using the PGDD database and the orthologous relationships were visualized using Circoletto. Amino acid content of the MR domain was calculated using the ‘Biostrings’ Bioconductor package. The putative cis-acting regulatory elements in the promoters were analyzed using custom Pyth […]

library_books

Next Generation Sequencing Analysis of the Human TCRγδ+ T Cell Repertoire Reveals Shifts in Vγ and Vδ Usage in Memory Populations upon Aging

2018
Front Immunol
PMCID: 5845707
PMID: 29559980
DOI: 10.3389/fimmu.2018.00448

[…] replicates 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 to the BioProjec […]

library_books

The role of transposable elements in functional evolution of amphioxus genome: the case of opsin gene family

2018
Sci Rep
PMCID: 5802833
PMID: 29410521
DOI: 10.1038/s41598-018-20683-9

[…] able ). For each opsin gene, orthologs from the three Branchiostoma species were aligned using ClustalO and visualized using BoxShade. In the case of orthologs absent from one or two species, we used Circoletto, in order to investigate synteny conservation and visualize sequence similarity among syntenic scaffolds from the Branchiostoma species. E-value for the BLAST run was set to e−20. […]

library_books

An RNA Virome Associated to the Golden Orb Weaver Spider Nephila clavipes

2017
Front Microbiol
PMCID: 5660997
PMID: 29118750
DOI: 10.3389/fmicb.2017.02097

[…] fa/phobius/. 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 with the RNA […]

library_books

Identification of Trans 4 Hydroxy L Proline as a Compatible Solute and Its Biosynthesis and Molecular Characterization in Halobacillus halophilus

2017
Front Microbiol
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 was […]

library_books

Complete Mitochondrial Genome of Phytophthora nicotianae and Identification of Molecular Markers for the Oomycetes

2017
Front Microbiol
PMCID: 5550686
PMID: 28848506
DOI: 10.3389/fmicb.2017.01484

[…] results among members of the oomycetes using Mauve software with default parameters (). The invert repeat structure was detected using the blastn program against the sequence itself and visualized in Circoletto (). […]


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

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