python版本MCScanX分析方法

python版本MCScanX分析方法 https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version)

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.chinenese and C.baccatum were retrieved from PGP (http://peppergenome.snu.ac.kr/download.php).The C. annuum genome was compared to C.chinenese and C.baccatum  genomes 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

[3] MCscan GitHub wiki https://github.com/tanghaibao/jcvi/wiki/MCscan-(Python-version) , GitHub, June 9th, 2018


参考文献:

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

attachments-2018-10-vYVqbsWz5bc545fb97a78.jpg

更详细的基因组共线性分析可观看:《基因家族分析实操课程》有详细操作说明



  • 发表于 2018-10-16 10:01
  • 阅读 ( 9377 )
  • 分类:文献解读

1 条评论

请先 登录 后评论
omicsgene
omicsgene

生物信息

654 篇文章

作家榜 »

  1. omicsgene 654 文章
  2. 安生水 325 文章
  3. Daitoue 167 文章
  4. 生物女学霸 120 文章
  5. 红橙子 78 文章
  6. CORNERSTONE 72 文章
  7. rzx 67 文章
  8. xun 66 文章