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Citations per year

Number of citations per year for the bioinformatics software tool MCScan

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This map represents all the scientific publications referring to MCScan per scientific context
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MCScan specifications


Unique identifier OMICS_11723
Name MCScan
Alternative name Multiple Collinearity Scan
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input data MCscan reads in at least two sources of data: .blast file and .bed file.
Operating system Unix/Linux
Computer skills Advanced
Version 0.8
Stability Stable
Maintained Yes


No version available



  • person_outline Haibao Tang

Publication for Multiple Collinearity Scan

MCScan citations


The grapevine kinome: annotation, classification and expression patterns in developmental processes and stress responses

PMCID: 5878832
PMID: 29619230
DOI: 10.1038/s41438-018-0027-0

[…] f tandemly duplicated genes was constructed using Mapchart 2.30 ( The segmental duplication events of grapevine kinases were determined using the MCScanX (Multiple Collinearity Scan, package. […]


Genome Wide Analysis Characterization and Evolution of SBP Genes in Fragaria vesca, Pyrus bretschneideri, Prunus persica and Prunus mume

Front Genet
PMCID: 5841269
PMID: 29552026
DOI: 10.3389/fgene.2018.00064

[…] In order to elaborate the precise region that containing SBP-box genes, Multiple Collinearity Scan toolkit (MCSscanX) was used to determine the microsynteny among these four species Strawberry (F. vesca), Chinese pear (Pyrus bretschneideri), Peach (Prunus persica), and Me […]


Divergence and evolution of cotton bHLH proteins from diploid to allotetraploid

BMC Genomics
PMCID: 5824590
PMID: 29471803
DOI: 10.1186/s12864-018-4543-y

[…] Duplicated bHLH pairs were extracted from the segmental duplication results. Pairs of duplicated regions that shared 6 or more duplicated genes (sm ≥ 6) in each pair of blocks were identified by MCSCAN ( Synonymous substitutions (Ks) were used to distinguish the recent and old duplicated pairs based on the WGD event.Expression data for GhbHLH g […]


Genome Wide Study of YABBY Genes in Upland Cotton and Their Expression Patterns under Different Stresses

Front Genet
PMCID: 5808293
PMID: 29467795
DOI: 10.3389/fgene.2018.00033

[…] nslocation within the GhYABBY6 locus occurred before upland cotton speciation. We found that GhYABBY11_Dt and GrYABBY11 are located on homologous chromosomes, whereas GaYBBY11 located on the scaffold.MCSCAN was used to determine the duplicate gene types. Five types of gene duplication may occur, namely, singleton, dispersed, proximal, tandem, and segmental duplication. Over half of the YABBY genes […]


Genome Wide Analysis of the NF YB Gene Family in Gossypium hirsutum L. and Characterization of the Role of GhDNF YB22 in Embryogenesis

Int J Mol Sci
PMCID: 5855705
PMID: 29415481
DOI: 10.3390/ijms19020483

[…] search tool (BLAST) [] was used to retrieve the GhNF-YB protein sequences from a local database. Next, these sequences were analysed to identify the collinearity blocks against the whole genome using MCSCAN ( [], while CIRCOS software ( was used to draw the collinearity map []. […]


Genome Wide Characterization of Heat Shock Protein 70s from Chenopodium quinoa and Expression Analyses of Cqhsp70s in Response to Drought Stress

PMCID: 5852552
PMID: 29360757
DOI: 10.3390/genes9020035

[…] tein sequences. To investigate HSP70 neighborhood microsynteny, the genome information of quinoa was used to detect the synteny and collinearity region for each Hsp70 gene in their own scaffolds with multiple collinearity scan toolkit (MCScanX) []. Protein sequences from quinoa proteome were aligned against protein sequences in quinoa using BLASTp with a maximum E-value of 1 ×10−20. High-confidenc […]

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MCScan institution(s)
Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, USA; Department of Plant Biology, University of Georgia, Athens, GA, USA; College of Science, Hebei Polytechnic University, Tangshan, Hebei, China; Department of Plant Biology, University of Illinois at Urbana–Champaign, Champaign, IL, USA; Advanced Studies in Genomics, Proteomics and Bioinformatics, University of Hawaii, Honolulu, HI, USA

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