Tair上拟南芥MADS-box基因的鉴定结果
https://www.arabidopsis.org/browse/genefamily/MADSlike.jsp
“We exploited a hidden Markov model that produces a profile out of a multiple sequence alignment. A profile for MADS-box proteins was built to screen the Arabidopis genome to identify new members of this family. Only hits with a E value of <1 were considered to be members of the family. This analysis resulted in 107 MADS-box proteins, which could be sub-divided in type-I (Malpha, Mbeta, Mgamma) and type-II (MIKC, Mdelta) family members.”
文章2003年发表在plant cell上。
文章地址:https://academic.oup.com/plcell/article/15/7/1538/6010075
先贴两张图放这儿
构树方法的描述(legend描述)“Protein maximum likelihood tree: The tree was constructed in the Bayesian framework using MrBayes software (Huelsenbeck, 2000) under the jtt substitution model with a γ distribution to accommodate differences of substitution rates between sites. Bootstrap proportions were calculated using programs within the PHYLIP package (Felsenstein, 1989).”
这一句话里包含了好多知识点,而以前看到这些词的时候我从来没有深究过,是时候好好学习一下了。
maximum likelihood tree:
看了两段,感觉已经有好多脑细胞阵亡了。
首先举了个例子,就是统计中一直用的投硬币的例子。假设正面朝上的概率是p。投了十次硬币的结果是“HTTHTHTHTT”【H head 正面朝上, T tail 反面朝上】 。那么得到“HTTHTHTHTT”这个结果的概率为:L(p) = Pr(D;p) = p(1 − p)(1 − p)p(1 − p)p(1 − p)p(1 − p)(1 − p) = p 4 (1 − p) 6 .
如何得到p,就是这个p,能使L(p)最大,这儿需要用到微积分。我不懂微积分,文章里是这么写的。通过不断的抛硬币实验,我们就可以得到无限接近真实结果的p.
那么这个方法是如何运用的构建进化树的呢?等我看懂了再写。谁来救救我。我最好找找中文的资料。
还真找到了,简述文章地址:最大似然法 (1)基本原理 - 简书 (jianshu.com)
legend描述:“The tree was constructed using the program MrBayes (Huelsenbeck, 2000), and the support values shown are Bayesian posterior probabilities. Branches with <50% support have been collapsed to give polytomies.”
构树支持率的问题:
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在ncbi上可以看到许多在其它物种中鉴定MADS-box的小文章,包括水稻,苹果,西红柿,西瓜等。
那MADS-box在整个植物界的进化情况呢?
2010年发表在MBE上的文章:
“MIKC* MADS-Box Proteins: Conserved Regulators of the Gametophytic Generation of Land Plants”
这难道是姐妹篇?
2012年发表在MBE:
“How MIKC* MADS-Box Genes Originated and Evidence for Their Conserved Function Throughout the Evolution of Vascular Plant Gametophytes”
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动物和植物都有MADS-box基因
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希望一个基因家族搞定所有基因家族研究的知识点
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裸子植物MADS-box基因
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