MCScanX pipeline

MCScanX specifications


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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  • person_outline Yupeng Wang <>

Publication for MCScanX

MCScanX IN pipelines

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 […]

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 (98) and calculated the percentage of obv-evg genes in these regions (i.e., cg in fig. s2b)., we used raw reads for the above assemblies, but the reads underwent a quality-control screening […]

PMCID: 5453933
PMID: 28572585
DOI: 10.1038/s41598-017-02860-4

[…] (msu7). then, the all-vs-all blastp69 was used to identify candidate duplicates and a gene pair that was top 5 matched and with an e-value < 10−10 was considered as a candidate duplicates. then, mcscanx70 was performed to categorize different types of duplicates, included wgd, tandem, proximal and transposed duplicates, with default parameters. finally, we only selected those duplicates […]

PMCID: 5469757
PMID: 28611446
DOI: 10.1038/s41598-017-03445-x

[…] cut-off was considered appropriate. for comparative genomics analysis of species-specific genes and clustering of orthologues, orthomcl (v2.0.9) was used110, 111. synteny analysis was performed in mcscanx112 by the pairwise determination of syntenic regions between species based on the order of orthologues from the orthomcl output with default values. b. canis contigs were arranged according […]

PMCID: 5603765
PMID: 28938721
DOI: 10.1093/gigascience/gix075

[…] genes in the p. pruinosa genome., table s9: functional annotation of predicted genes for p. pruinosa., table s10: summary of syntenic blocks between p. pruinosa and p. euphratica identified using mcscanx., table s11: top 10 go categories (biological process and molecular function) displaying the highest ka/ks ratios between p. pruinosa and p. euphratica., table s12: summary of gene family […]

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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