MCScan protocols

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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


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  • person_outline Haibao Tang <>

Publication for Multiple Collinearity Scan

MCScan in pipelines

PMCID: 5449364
PMID: 28560587
DOI: 10.1186/s12284-017-0164-3

[…] chromosome. segmental duplications were identified using the plant genome duplication database (pgdd) (lee et al. ). collinear blocks within the o. sativa subsp. japonica genome were determined by mcscan v8 (, the output data was downloaded and searched for presence of lectin genes. duplicated genes with a ks (synonymous substitution) value […]

PMCID: 5400374
PMID: 27856652
DOI: 10.1093/molbev/msw242

[…] 10 species were retained., in addition, 3863 single copy nuclear genes that were shared by four species (fragaria vesca, prunus persica, prunus mume, and cucumis sativus) were identified by using mcscan v0.8 (). to avoid selecting the same genes, the 3863 orthologs were identified in arabidopsis thaliana, and by comparing gene ids, those overlapping with the above-mentioned 4180 gene set […]

PMCID: 4340835
PMID: 25759239
DOI: 10.1186/s12864-015-1293-y

[…] provided in the lis database [] were utilized for plotting the genes on the eight chickpea chromosomes and visualized using mapchart []. collinear blocks with e-value ≤ 1e−10 were identified by mcscan [] from the plant genome duplication database [] and f-box genes falling in these blocks were considered as segmentally duplicated. genes separated by 10 or fewer genes and >50% similarity […]

PMCID: 4013592
PMID: 24705465
DOI: 10.3390/ijms15045730

[…] genes were defined as adjacent to homologous zhd genes on the grape chromosomes or within a sequence distance of 50 kb [], with no more than one intervening gene []. for synteny analysis, we used mcscan algorithm for detection of synteny and collinearity []. synteny blocks within the grape genome and between the grape and arabidopsis genomes were downloaded from the plant genome duplication […]

PMCID: 4089393
PMID: 24136039
DOI: 10.1038/ncomms3640

[…] each species, using an e-value cutoff of 1e-10, coverage ≥50% and identity ≥20%. syntenic regions within each species and between kiwifruit and grape, tomato and potato were then identified using mcscan based on the all-to-all blastp results. protein sequences of homologous gene pairs in the identified syntenic regions were first aligned using muscle, and the protein alignments […]

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MCScan in publications

PMCID: 5847563
PMID: 29531231
DOI: 10.1038/s41598-018-22585-2

[…] and visualized by using gsds 2.0 ( the duplication pattern of each sigols and sirs gene was analyzed using mcscanx software ( according to the previous description. conserved motifs in sigolss and sirss were identified using meme v4.11.4 (, to measure the transcript levels […]

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

[…] dna sequences and coding domain sequences (cds) were used in gene structure display server tool to determine gene structure., 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), […]

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

[…] t-test, p ≤ 0.05, additional file ). we found slightly more genes with expression bias toward the d-homoeologs than the a-homoeologs, which is consistent with the published data [].fig. 2, using mcscan (, we detected 10,393 and 11,781 pairs of duplicated genes in the a- and the d-subgenome chromosomes, respectively based on the whole genome […]

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

[…] yabby protein sequences of upland cotton were aligned with each other using the basic local alignment search tool (blast) with a cut-off e-value of 1 × 10−5. the blastp results were analyzed using mcscan software to produce collinearity blocks across the whole genome. collinear pairs within the yabby family of proteins were extracted to draw a collinearity map using circos software (krzywinski […]

PMCID: 5855705
PMID: 29415481
DOI: 10.3390/ijms19020483

[…] 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 []. , using clustal x 2.0 […]

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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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