SynChro statistics

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Citations per year

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

This map represents all the scientific publications referring to SynChro per scientific context
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Protocols

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

Versioning


No version available

Maintainer


  • person_outline Guénola Drillon

Publications for SynChro

SynChro citations

 (11)
library_books

Inferring synteny between genome assemblies: a systematic evaluation

2018
BMC Bioinformatics
PMCID: 5791376
PMID: 29382321
DOI: 10.1186/s12859-018-2026-4

[…] The four anchor-based programs DAGchainer [], i-ADHoRe [] (v3.0), MCScanX [] and SynChro [], and the nucleotide alignment-based Satsuma [], were used to identify synteny blocks. Settings for each program were modified to resemble each other on the results of C. elegans vs. C. eleg […]

library_books

Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca

2018
Sci Rep
PMCID: 5772498
PMID: 29343788
DOI: 10.1038/s41598-017-18378-8

[…] matic 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 orth […]

library_books

Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data

2017
Sci Rep
PMCID: 5680185
PMID: 29123238
DOI: 10.1038/s41598-017-15484-5

[…] ncestral reconstruction approaches. They newly sequenced ten yeast species in the Lachancea genus and used software AnChro to reconstruct the ancestral genomes on the Lachancea genus level. They used SynChro to identify conserved syntenic blocks based on the DNA sequence information and additional parameters. They used ReChro to identify cycles of breakpoints for each pairwise combination of genom […]

library_books

Genome Based Analyses of Six Hexacorallian Species Reject the “Naked Coral” Hypothesis

2017
Genome Biol Evol
PMCID: 5737686
PMID: 29048525
DOI: 10.1093/gbe/evx196

[…] to the phylogenetic distance and the dearth of conserved synteny groups in the H. magnipapillata genome, we omitted the outgroup from this analysis. Briefly, we first identified synteny blocks using SynChro () with different block stringency parameters (Delta 1–6). In the following step, we analyzed the different outputs using PhyChro to identify “incompatible” block adjacencies between all genom […]

library_books

Genome sequence of the type strain CLIB 1764T (= CBS 14374T) of the yeast species Kazachstania saulgeensis isolated from French organic sourdough

2017
Genom Data
PMCID: 5501885
PMID: 28725555
DOI: 10.1016/j.gdata.2017.07.003

[…] ricana 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 are […]

call_split

Effects of an Intensive Lifestyle Intervention to Treat Overweight/Obese Children and Adolescents

2017
Biomed Res Int
PMCID: 5474545
PMID: 28656151
DOI: 10.1155/2017/8573725
call_split See protocol

[…] s plus 30 minutes of circuit training for muscular strength. The cardiovascular activity was performed using ergometers (Run 500, Runrace 1200 Hc, Bike Race, Recline 600 Xt Pro, and Top 600xt Pro and Synchro, Technogym, Cesena, Italy). The intensity of the exercises was gradually increased (5% every three weeks) starting from 50% of heart rate reserve (HRR) calculated by Karvonen's formula to reac […]


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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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