Cyntenator statistics

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Cyntenator specifications


Unique identifier OMICS_11705
Name Cyntenator
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes


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  • person_outline Christoph Dieterich <>

Publication for Cyntenator

Cyntenator in pipeline

PMCID: 4488370
PMID: 26125626
DOI: 10.1371/journal.pone.0131136

[…] and deletions, we restricted the analysis to conserved syntenic regions between the reference strain and the sister species p. exspectatus. we defined conserved syntenic regions using the program cyntenator []. we used a sufficiently high gap and mismatch penalties (-gap -1000 -mis -1500) to ensure that gene orders between both genomes is the same (perfectly collinear). in addition […]

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Cyntenator in publications

PMCID: 5495381
PMID: 28671949
DOI: 10.1371/journal.pone.0180198

[…] non-overlapping segments and the fourth repairs incorrect ruptures of synteny. all these refinements are implemented in a new version of phyldiag that has been benchmarked against i-adhore 3.0 and cyntenator, based on a realistic simulated evolution and true simulated conserved segments., the pre- and post-processing steps have been implemented in the python library libsdyogen. these steps […]

PMCID: 4987105
PMID: 27289092
DOI: 10.1093/gbe/evw133

[…] from zootermopsis nevadensis (isoptera). in the case of d. melanogaster, we used the longest isoform per gene for further analysis. conserved synteny between beetle genomes was detected by means of cyntenator software (), which computes gene order alignments using a phylogenetic scoring function. this approach identified conserved syntenic blocks between o. borbonicus and the t. castaneum […]

PMCID: 4603330
PMID: 26449933
DOI: 10.1186/1471-2164-16-S10-S8

[…] in a similar way., there are many programs designed to find synteny (or syntenic) blocks in the comparison of two or more eukaryotic gene orders, e.g., i-adhore [], dagchainer [], cinteny[], cyntenator [], mcscan [] and drimm-synteny []. these differ in search strategy, flexibility, performance and interpretation. synmap is based on the dagchainer algorithm, and balances sensitivity […]

PMCID: 4223023
PMID: 25375783
DOI: 10.1371/journal.pone.0112341

[…] with a class of orthology-based tools suitable for the identification of small blocks of conserved gene order, or collinear blocks, which usually work on a genome-wide scale. similar to our tool, cyntenator , mcscanx and i-adhore identify regions of conserved gene order by applying alignment techniques to a set of ortholog anchors such as genes. these methods are in principle suitable […]

PMCID: 4138177
PMID: 25137074
DOI: 10.1371/journal.pone.0105015

[…] popular synteny tools such as i-adhore 3.0 and mcscanx can efficiently detect homologous regions even in large-scale analyses. otherwise, using local alignments of sequences, tools such as cyntenator and dagchainer allow for detection of syntenic regions based on pairwise similarity scores of sequence intervals. the heuristic method ffadj-mcs has proven to be a good compromise […]

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Cyntenator institution(s)
The Max Planck Society, Germany; the Helmholtz Society, Germany
Cyntenator funding source(s)
Institute for Medical Genetics, Charité-Universitätsmedizin, Berlin, Germany; Max Planck Institute for Molecular Genetics, Berlin, Germany; Bioinformatics in Quantitative Biology, Berlin Institute for Medical Systems Biology, Berlin, Germany

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