MCScanX protocols

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MCScanX specifications

Information


Unique identifier OMICS_11717
Name MCScanX
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Requirements
Xcode, JDK, libpng
Maintained Yes

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Documentation


Maintainer


  • person_outline Yupeng Wang <>

Publication for MCScanX

MCScanX in pipelines

 (24)
2018
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] (supplementary file : table s7) using mega v6.0 with the maximum-liklihood algorithm (tamura et al., )., syntenic blocks between the genomes of a. ipaensis and other plants were identified using the mcscanx with default parameters (wang et al., ) and visualized on the genome using circos (krzywinski et al., ). genomic sequences were first aligned annotated genes based on amino acid sequence […]

2018
PMCID: 5944053
PMID: 29743014
DOI: 10.1186/s12864-018-4744-4

[…] their relationships were constructed using cytoscape (v3.6.0) []. first, whole-genome protein sequences from all species were searched against themselves using blastp with an e-value of 1 × 10− 5. mcscanx v1.0 (−k 50, −s 5, −m 25) was then used to detect the duplicated type and collinear blocks according to a previous report []. then, we extracted the bes1 genes located in the collinear blocks […]

2017
PMCID: 5223533
PMID: 28068923
DOI: 10.1186/s12864-016-3454-z

[…] [] with an e-value cutoff of 10−5 and parsed out top five hits. the core-orthologous genes were defined by orthomcl []. the colinearity blocks between two oryza species were calculated by software mcscanx with default parameters []., go terms associated with genes of the cultivated and wild rice species were used to perform enrichment analysis of genes with or without tes, including gene […]

2017
PMCID: 5332604
PMID: 28261669
DOI: 10.1128/mSphere.00359-16

[…] best hits of blastp; e value, <1e−5) with the genome in the comparison. cg corresponds to the percentage of genes in each obv-evg that are present in colinearity regions as determined by mcscanx with default settings. these dot plots are sorted by bg (from upper left to bottom right on three pages). all tblastx alignments are shown. the sequences in the dot plots are circularly […]

2017
PMCID: 5332604
PMID: 28261669
DOI: 10.1128/mSphere.00359-16

[…] genomic colinearity. eighteen obv-evgs (39%) were observed to exhibit complete or nearly complete colinearity with other viral genomes. additionally, we identified colinear genomic regions using mcscanx () and calculated the percentage of obv-evg genes in these regions (i.e., cg in )., we used raw reads for the above assemblies, but the reads underwent a quality-control screening […]


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MCScanX in publications

 (154)
PMCID: 5944053
PMID: 29743014
DOI: 10.1186/s12864-018-4744-4

[…] their relationships were constructed using cytoscape (v3.6.0) []. first, whole-genome protein sequences from all species were searched against themselves using blastp with an e-value of 1 × 10− 5. mcscanx v1.0 (−k 50, −s 5, −m 25) was then used to detect the duplicated type and collinear blocks according to a previous report []. then, we extracted the bes1 genes located in the collinear blocks […]

PMCID: 5944045
PMID: 29743013
DOI: 10.1186/s12864-018-4722-x

[…] chromosome was calculated using a perl script. then, we made a diagram of the gras members that showed duplications among 26 chromosomes and identified five types of gene duplication events with mcscanx using the gras protein sequences and the position data in chromosomes []. additionally, we made a diagram of the chromosomal locations with the mapinspect software []., the protein sequences […]

PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] (supplementary file : table s7) using mega v6.0 with the maximum-liklihood algorithm (tamura et al., )., syntenic blocks between the genomes of a. ipaensis and other plants were identified using the mcscanx with default parameters (wang et al., ) and visualized on the genome using circos (krzywinski et al., ). genomic sequences were first aligned annotated genes based on amino acid sequence […]

PMCID: 5915607
PMID: 29691383
DOI: 10.1038/s41467-018-03423-5

[…] table ). pcr products were verified by agarose gel electrophoresis (supplementary figs.  and )., a homolog search within the g. elata genome was performed using blastp (e-value < 1e−7), and mcscanx was used to identify syntenic blocks within the genome. for each gene pair in a syntenic block, the 4dtv (transversion substitutions at fourfold degenerate sites) distance was calculated, […]

PMCID: 5924566
PMID: 29690608
DOI: 10.3390/genes9040224

[…] p. bretschneideri and p. communis genomes, with an e-value below 1 × 105. according to the results of blastp and gff, we determined the genome-wide duplication (gwd)/segmental duplication using mcscanx software []. the ka (non-synonymous substitution)/ks (synonymous substitution), ka, and ks values were estimated using dnasp 5.0 software []. the microcollinearity visualization […]


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MCScanX institution(s)
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA; Institute of Bioinformatics, University of Georgia, Athens, GA, USA; Department of Plant Biology, University of Georgia, Athens, GA, USA; J. Craig Venter Institute, Chinakville, MD, USA; Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA; Center for Genomics and Computational Biology, School of Life Sciences and School of Sciences, Hebei United University, Tangshan, Hebei, China; Department of Genetics and 8Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
MCScanX funding source(s)
National Science Foundation (NSF: DBI 0849896, MCB 0821096, MCB 1021718); National Institutes of Health (R01 AI068908) in part; resources and technical expertise from the University of Georgia, Georgia Advanced Computing Resource Center in part

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