Cinteny protocols

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Cinteny specifications

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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 in pipelines

 (2)
2018
PMCID: 5851622
PMID: 29538447
DOI: 10.1371/journal.pone.0194335

[…] 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 (http://cinteny.cchmc.org/)[] is used to analyze synteny and evolutionary distances in terms of genome rearrangements for selected organisms. cinteny server allows comparing multiple […]

2013
PMCID: 3828384
PMID: 24244720
DOI: 10.1371/journal.pone.0080824

[…] 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 (http://cinteny.cchmc.org/) and genomicus server were used for syntenic analysis., zebrafish mrna was isolated from 24 and 48 hpf old embryos using the trizol/phenol-chloroform method. […]


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Cinteny in publications

 (10)
PMCID: 5851622
PMID: 29538447
DOI: 10.1371/journal.pone.0194335

[…] 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 (http://cinteny.cchmc.org/)[] is used to analyze synteny and evolutionary distances in terms of genome rearrangements for selected organisms. cinteny server allows comparing multiple […]

PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] motifs identified by meme ()., to identify conserved syntenic regions, genes flanking c9orf72 in human, mouse and fugu were annotated. initial predictions were derived from the online server cinteny () (http://cinteny.cchmc.org/) and the synteny database (). the programs identify syntenic regions across the genomes selected for comparison and analyse the extent of genome rearrangement […]

PMCID: 5740759
PMID: 29268782
DOI: 10.1186/s40246-017-0131-5

[…] project of human (figure 46 of []), brown norway rat (figure 4 of []), and taurine cattle (figure s12 of []). to further investigate the synteny of human 8q in mouse, rat, and bovine, the tool cinteny [] was used to visualize the extent of synteny and they can be found in additional file : figure s2., there are two possible explanations to account for the observed syntenic conservation […]

PMCID: 5598925
PMID: 28910296
DOI: 10.1371/journal.pone.0179112

[…] confidence scoring of ppis, thus, in turn, refining the general ppi map used in studies like these., 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) […]

PMCID: 4717579
PMID: 26782621
DOI: 10.1186/s13064-015-0056-4

[…] and any new membrane extensions were counted for each frame. the percent protrusions for each section was then calculated and plotted in mathematica v9 (wolfram)., performed using synteny (http://cinteny.cchmc.org/)., instat (graphpad) was used to run statistical analysis on data sets. student’s t-test, anova followed by bonferroni or kruskal-wallis test followed by dunn’s post-hoc test […]


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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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