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MicroSyn specifications

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Unique identifier OMICS_11711
Name MicroSyn
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages C#
Computer skills Medium
Stability No
Requirements
Net framework
Maintained No

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Publication for MicroSyn

MicroSyn citations

 (9)
library_books

Characterization and expression of the ABC family (G group) in ‘Dangshansuli’ pear (Pyrus bretschneideri Rehd.) and its russet mutant

2018
PMCID: 5901498
PMID: 29658971
DOI: 10.1590/1678-4685-GMB-2017-0109

[…] blastp hits were scanned for abcg domains using interproscan., the chromosome number is indicated on the chromosome. the synteny relationship between each pair of abcg genes was detected using the microsyn software and positioned on the 17 pear chromosomes. the pbabcg gene names were assigned according to their position on pear chromosomes 1-17. the chromosome map showing the physical location […]

library_books

Retention and Molecular Evolution of Lipoxygenase Genes in Modern Rosid Plants

2016
PMCID: 5043136
PMID: 27746812
DOI: 10.3389/fgene.2016.00176

[…] selection acts upon specific sites, the gene pairs for all the paralogs and orthologs were used to calculate the ω, where ω = ka/ks., microsynteny analysis within four species was detected by microsyn software (cai et al., ). at the beginning of the generated msy file step, three property files are needed: the gene list file, the cds file and the gene identifier file. the microsynteny […]

library_books

Evolutionary and functional analysis of mulberry type III polyketide synthases

2016
PMCID: 4973071
PMID: 27487946
DOI: 10.1186/s12864-016-2843-7

[…] bootstrap analysis with 1,000 resampling replicates., all scaffolds that contained putative mulberry type iii pks genes were analyzed. the microsyntenic regions surrounding genes were detected using microsyn software []. the mean ks value was calculated for all pairs of protein-coding genes among all genomic fragments using the method described by nei and gojobori []. the timing of gene […]

library_books

Molecular evolution and expression divergence of the Populus euphratica Hsf genes provide insight into the stress acclimation of desert poplar

2016
PMCID: 4948027
PMID: 27425424
DOI: 10.1038/srep30050

[…] for duplication of hsf genes in p. euphratica and s. suchowensis, the duplicated events were identified based on the duplicated block from synteny analysis using microsyn. a duplicated block was defined as a region where three or more conserved homologs were located within 15 genes up- and down-stream between scaffolds., the cis-acting elements in promoter […]

library_books

Characterization and Comparison of the CPK Gene Family in the Apple (Malus × domestica) and Other Rosaceae Species and Its Response to Alternaria alternata Infection

2016
PMCID: 4871508
PMID: 27186637
DOI: 10.1371/journal.pone.0155590

[…] to examine the relative contribution of these kinds of mechanisms in the expansion of the cpk gene family in rosaceae, we detected the origins of duplicate genes for the cpk gene family using the microsyn package[]. different patterns of gene duplication contributed differentially to the expansion of the cpk gene family in the investigated species (). remarkably, 15cpk genes in apple […]

library_books

Genome wide analysis of WRKY transcription factors in white pear (Pyrus bretschneideri) reveals evolution and patterns under drought stress

2015
PMCID: 4691019
PMID: 26704366
DOI: 10.1186/s12864-015-2233-6

[…] the gff file using a programmed perl script. genes within a maximum of 10 genes distance were considered to be tandem duplicates. the microsyntenies between each pair of members were detected using microsyn software []. the parameters were set as follows: window size of 50 genes, tandem gap value of 2, expected threshold value cut off of 0.01, and three homologous pairs to define a syntenic […]


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MicroSyn institution(s)
College of Horticulture, Nanjing Agricultural University, Nanjing, China; Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA; Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA; BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, USA

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