Cinteny statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Cinteny

Tool usage distribution map

This map represents all the scientific publications referring to Cinteny per scientific context
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Cinteny specifications


Unique identifier OMICS_00931
Name Cinteny
Interface Application programming interface
Restrictions to use Academic or non-commercial use
Programming languages C++, PHP
License GNU General Public License version 3.0
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Cinteny

Cinteny citations


Molecular evolution and functional divergence of eukaryotic translation initiation factor 2 alpha kinases

PLoS One
PMCID: 5851622
PMID: 29538447
DOI: 10.1371/journal.pone.0194335

[…] ucture. Representative gene sequences of each phyla of animal kingdom are submitted to GSDS server for generating visualization of gene features such as composition and position of exons and introns. Cinteny server ([] is used to analyze synteny and evolutionary distances in terms of genome rearrangements for selected organisms. Cinteny server allows comparing multiple ge […]


The impact of the protein interactome on the syntenic structure of mammalian genomes

PLoS One
PMCID: 5598925
PMID: 28910296
DOI: 10.1371/journal.pone.0179112
call_split See protocol

[…] Orthology-based conserved syntenic blocks were defined in two steps with an approach inspired by Cinteny [], SyntenyTracker [] and i-ADHoRe [,]. First, pairwise syntenic blocks were defined by comparing the order of orthologous protein-coding genes in the human genome (assembly GRCh37.p8) with th […]


Syntenic block overlap multiplicities with a panel of reference genomes provide a signature of ancient polyploidization events

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

[…] 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 sensit […]


Identification and Expression Analysis of Zebrafish Glypicans during Embryonic Development

PLoS One
PMCID: 3828384
PMID: 24244720
DOI: 10.1371/journal.pone.0080824
call_split See protocol

[…] ysis. ClustalW and the Jalview software were used for generating and viewing the multiple sequence alignment, respectively. Protein sequence similarity and identities were obtained using NCBI BLASTp. Cinteny server ( and genomicus server were used for syntenic analysis. […]


What google maps can do for biomedical data dissemination: examples and a design study

BMC Res Notes
PMCID: 3658873
PMID: 23642009
DOI: 10.1186/1756-0500-6-179

[…] lusterview [], Hierarchical Clustering Explorer (HCE) [], and Spotfire [], systems for pathway and network analysis like Cytoscape [], VisANT [], Ingenuity [] and Patika [], or genome viewers such as Cinteny [] and Mizbee []. Most such systems are aimed at complex data exploration and analysis and have associated overhead costs such as deploying, learning and operating the systems, data formatting […]


Large Scale Functional Organization of Long Range Chromatin Interaction Networks

Cell Rep
PMCID: 4181841
PMID: 23103170
DOI: 10.1016/j.celrep.2012.09.022

[…] e., the number of interactions per Mb) within genomic blocks that were syntenic or nonsyntenic to chimp and mouse genomes. We used a moderate level of coarse graining to map syntenic blocks using the Cinteny algorithm () (), which revealed human-chimp and human-mouse syntenic blocks covering 48% and 45% of the human genome, respectively. Subsequent analysis revealed a nonrandomly higher density of […]

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Cinteny institution(s)
Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA; Department of Environmental Health, University of Cincinnati College of Medicine, Cincinnati, OH, USA; Department of Informatics, Nicholas Copernicus University, Torun, Poland
Cinteny funding source(s)
This work has been supported by NIH grants R21 AI055338 and R01 AR050688.

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