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|Interface||Command line interface|
|Restrictions to use||None|
|Operating system||Unix/Linux, Mac OS|
Xcode, JDK, libpng
No version available
- Documentation: http://chibba.pgml.uga.edu/mcscan2/documentation/manual.pdf
- person_outline Yupeng Wang
Publication for MCScanX
Comprehensive analyses of the BES1 gene family in Brassica napus and examination of their evolutionary pattern in representative species
[…] contributed the most to the expansion of this gene family in many plant lineages. We examined 5 types of gene duplications: singleton, dispersed, proximal, tandem, and WGD or segmental duplication by MCScanX program (Table , Additional file : Table S3). The percentage of WGD was 75.0% in B. napus, B. rapa (80.0%), B. oleracea (84.6%), and A. thaliana (62.5%) (Table ). However, WGD or segmental dup […]
Genome wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L.
[…] each 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 . […]
Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)
[…] erplot (Delcher et al., ) and Gunplot 5.0 (www.gnuplot.info/). Ks values of the homologs within collinearity blocks were calculated using the perl script, add_ka_and_ks_to_collinearity.pl included in MCScanX package, and the median of Ks values was considered to be a representative of the collinearity blocks. […]
Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species
[…] Syntenic regions within and between genomes were identified using MCScanX , calling collinear ‘blocks’ regions with at least 5 homologous genes and fewer than 10 ‘gaps’ (i.e., missing genes). Rates of synonymous (KS) and nonsynonymous (KA) substitution between pai […]
The Gastrodia elata genome provides insights into plant adaptation to heterotrophy
[…] 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, and […]
Genome Wide Identification, Evolutionary, and Expression Analysis of VQ Genes from Two Pyrus Species
[…] tions and genome evolution among species. To gain insight into the evolution of P. bretschneideri and P. communis VQ motif-containing genes, the syntenic blocks were searched in the chromosomes using MCScanX software. Among them, 31 orthologous pairs were identified within these pairwise syntenic blocks ( and ). Additionally, we also observed a reciprocal homology in syntenic blocks between the P. […]
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