python分析方法_python版本MCScanX分析方法

python版本MCScanX分析方法，仅供参考：

Genomic synteny

among C. annuum, C.chinenese and C.baccatum

The genomes of C. annuum, C.chineneseandC.baccatum were retrieved from PGP ().TheC. annuumgenome was compared

toC.chineneseand C.baccatumgenomes using the MCScan toolkit (V1.1)[1].

To call synteny blocks, we performed all-against-all LAST [2] and

chained the LAST hits with a distance cutoff of 20 genes, also requiring at

least 4 gene pairs per synteny block. Chromosome-scale synteny blocks plots

were constructed using the python version of MCScan[3].

[1] Tang H, Wang X,

Bowers JE, et al. Unraveling ancient hexaploidy through multiply-aligned

angiosperm gene maps. Genome Res 2008;18(12):1944–54.

[2] S. M. Kiełbasa, R. Wan, K.

Sato, P. Horton, M. C. Frith, Adaptive seeds tame genomic sequence comparison.  Genome Res. 21, 487–493 (2011). Medline

doi:10.1101/gr.113985.110

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