在生物学中,保守序列(conserved sequence)是指在核酸序列/蛋白质序列/蛋白质结构/多聚糖序列内相似或相同的序列,这种情况可以发生在各物种间(种间同源序列)或由相同生物产生的不同分子(种内同源序列)间。对于物种间保守的情况,这意味着尽管物种形成一些特定的序列仍在进化过程中被保留了下来。
–维基百科定义
在研究某一蛋白的时候,查看同源蛋白的保守序列是十分基础的分析手段。一般来说,我们会制作黑白的保守序列对比图。这样的对比图只给出三种颜色,黑色,代表完全一致的氨基酸序列;灰色,代表相似氨基酸(比如GAVLI,脂肪族氨基酸,aliphatic amino acids);白色,代表完全不一致的氨基酸。黑白对比图,给出的信息更为直观,当我们看到序列有纯黑色背景的时候,就可以确定是完全一致的同源序列。当然,如果为了获取更为详细的对比信息,可制作彩色保守序列对比图,这样可以将相似氨基酸以更细致的方式区分开来,当然,一般的彩色对比图会包含七到八种颜色,看起来十分缭乱。制作什么样的对比图,完全取决于你的需要,本文仅介绍如何制作黑白对比图。
如何做出封面图一样的黑白保守序列对比图呢?BioEngX小编为大家提供一种不涉及使用任何序列分析软件,只使用两个网站的方法,这个方法分三步完成,用时不超过五分钟,能最快地帮助我们知道序列之间的同源片段在哪里。如果想要不仅仅做出保守序列,而且提供其他高级的分析功能,恐怕只有序列分析软件能够做到了,比如说:BioEdit。
1准备序列
准备好要分析的蛋白序列,并用fasta的格式排列在空文档中
>蛋白1
蛋白1的序列内容
>蛋白2
蛋白2的序列内容
>蛋白3
蛋白3的序列内容
依此类推,有多少个蛋白都可以列出来。
2多重序列对比, Clustal Omega
使用网站:http://www.ebi.ac.uk/Tools/msa/clustalo/
其实就是EBI网站上的多重序列对比服务,都是线上的网页程序,十分高效。
将列好的序列输入进行多重序列重合对比,记得在数据输出格式的时候勾选Pearson/FASTA格式,如下图所致:
等待30s,页面会自动刷新,给出多重序列重合对比的结果,将所得结果勾选并复制。
3制作黑白保守序列, SMS
使用网站:http://www.bioinformatics.org/sms2/color_align_cons.html
将刚复制的结果粘贴到输入框中,图内红框的部分:
点击Submit,等待2秒,制作就完成了,如下图所示,左边显示每条蛋白序列的名称(蓝框所示),右边显示序列位置(绿框所示)。
如果序列都已经准备好了,整个过程大概用时不超过5分钟,十分的方便。
如果你想制作彩色对比而不是黑白对比,可以试一试另外一个网站:http://www.bioinformatics.org/sms2/color_align_prop.html,使用方法和上文描述的一致。
快来试试吧~
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