关于metagenomics KEGG注释的时候如何去除真核结果

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(Edited)

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今天师妹问了我这个问题,思考之后,总结如下:

方法 1:

“All high-quality reads were aligned with Bowtie2 to the KEGG database 2014 (59), from which sequences of eukaryotes were excluded”
Zhaoliping 老师Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes文章中是这么做的。

但是,我们没有KEGG数据库,这个数据库需要购买 ,我找了一下,没有找到可以直接下载每一个KO对应的蛋白/核酸序列信息。
所以替代方法是,将蛋白序列(特别是能够比对到KO的序列)放到NCBI-BLASTP中比对nr数据库,它会得到比对到物种的信息。我们看这段序列比对到了什么 Eukaryotes 还是 Prokaryotes ,或者是两者都有。这样就间接判定了这段蛋白序列对应的KO是Prokaryotes还是Eukaryotes。

方法 2:

不通过比对得到。直接通过数据库中的信息,得到哪些pathway是Prokaryotes,哪些是Eukaryotes,哪些是两者共有。在目前的注释结果中删除Eukaryotes特有即可。(直接删除可能需要在富集分析前就删除,即删除后,再做富集分析。)

方法是利用KEGG的API得到我们想要的数据。
首先,http://rest.kegg.jp/list/organism 可以得到KEGG中收入的所有物种信息(包括是Eukaryotes或是Prokaryotes),然后,下载每一个物种对应含有的pathway ,如:http://rest.kegg.jp/list/pathway/T05351 最后,合并Prokaryotes的所有pathway,并去冗余。Eukaryotes,同样处理。取交集,得到overlap pathway。



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