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SynChro specifications

Information


Unique identifier OMICS_11718
Name SynChro
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The minimum input information that must be provided to SynChro is a list of protein-coding genes, ordered along the chromosomes (or scaffolds) and their associated amino-acid sequences. Their coordinates along chromosomes, centromere positions, and other genomic features are useful information but not compulsory for synteny block reconstruction.
Operating system Unix/Linux, Mac OS
Programming languages Python
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Guénola Drillon <>

Publications for SynChro

SynChro in pipeline

2016
PMCID: 4823976
PMID: 26733577
DOI: 10.1093/gbe/evv262

[…] diversity, was calculated with variscan ()., synteny conservation analysis of l. quebecensis ll2013_164 (cbs 14088), l. thermotolerans cbs 6340t, and lachancea waltii cbs 6430t was performed with synchro ()., all l. quebecensis isolates in this study were subjected to growth on a total of 33 different media types, the specific composition of each medium can be found in . the conditions tested […]


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SynChro in publications

 (6)
PMCID: 5772498
PMID: 29343788
DOI: 10.1038/s41598-017-18378-8

[…] annotation server (kaas) with bbh method. conserved syntenic regions between the two nuclear genomes of p. stagnora, p. cutis, and a. protothecoides were searched using the chronicle program of synchro (january 2015). for this analysis, we applied 7, 9, and 19 long scaffolds (>300 kb) of p. stagnora, p. cutis, and a. protothecoides, respectively. syntenic blocks, including more than two […]

PMCID: 5737686
PMID: 29048525
DOI: 10.1093/gbe/evx196

[…] then clustered using the “average hclust” method and node supports were calculated using the r package pvclust as described above., synteny conservation analyses were performed using the programs synchro () and phychro from the chronicle package (). in a first step we identified synteny blocks with synchro using multiple “delta” (block stringency parameter) values ranging from 1 to 6. […]

PMCID: 5501885
PMID: 28725555
DOI: 10.1016/j.gdata.2017.07.003

[…] and kazachstania naganishii, to investigate chromosome colinearity between k. saulgeensis and these species . we examined the synteny based on the presence and order of orthologous genes using synchro , with delta = 4 to minimize artifactual synteny breaks. this showed that rearrangements that have occurred since the last common ancestor of k. saulgeensis, k. africana and k. naganishii […]

PMCID: 4479816
PMID: 26108467
DOI: 10.1038/srep11571

[…] trees were reconstructed using phyml v2.4.4 with the wag model. bootstrap analysis was used to obtain branch support. trees were visualized with njplot., conserved synteny blocks were defined using synchro with default settings. first, reciprocal blast hits were computed with a similarity threshold of 40% and length ratio between the two protein sequences smaller than 1.3. second, syntenic […]

PMCID: 4316626
PMID: 25532815
DOI: 10.1093/gbe/evu273

[…] settings (http://mfold.rit.albany.edu//?q=mfold/dna-folding-form, last accessed december 19, 2014; ). synteny analyses for rover and roamer insertion site conservation were performed with chronicle/synchro (, available at http://www.lgm.upmc.fr/chronicle/synchro.html, last accessed december 19, 2014), with a delta parameter of 2 or 4, meaning that two adjacent genes are separated by less […]


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SynChro institution(s)
Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Biologie Computationnelle et Quantitative, Paris, France; CNRS, UMR7238, Biologie Computationnelle et Quantitative, Paris, France; Institut Universitaire de France, Paris, France
SynChro funding source(s)
This work was supported by the Agence Nationale de la Recherche (‘GB-3G’, ANR-10-BLAN-1606-01) and by an ATIP grant from the CNRS.

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