MicroSyn protocols

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MicroSyn specifications

Information


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 in pipeline

2015
PMCID: 4320540
PMID: 25636232
DOI: 10.1186/s12864-015-1242-9

[…] was used to analyze protein statistics, and the solubility of recombinant proteins was predicted by the rpsp program (http://biotech.ou.edu) []. the synteny of the bradof genes was calculated by microsyn software according to cai’s means (http://fcsb.njau.edu.cn/microsyn/) []., orthomcl was used to search for orthologous and paralogous genes in chinese cabbage, arabidopsis, and rice using […]


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MicroSyn in publications

 (9)
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 […]

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 […]

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 […]

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 […]

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 […]


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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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