MCScan protocols

MCScan computational protocol

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 pipeline

PMCID: 3320632
PMID: 22496844
DOI: 10.1371/journal.pone.0034701

[…] an ortholog if the following two conditions are met: 1) x is the reciprocal best match of y and 2) x is located in a syntenic block where y is found. syntenic regions were established using multiple collinearity scan [58], with 1e−5 as an alignment significance threshold, match size ≥5, and average intergenic distance., the full-length protein sequences of pscrxlr1 and its orthologs […]

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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