OrthoFinder
2023-05-29 本文已影响0人
LET149
https://www.jianshu.com/p/3d0051edde97?utm_campaign=haruki&utm_content=note&utm_medium=seo_notes&utm_source=recommendation
https://www.jianshu.com/p/16e0bbb2ba19
1. 将需要进行比对物种(2个或者以上)的蛋白质fasta数据放在同一个目录下
(base) zhiyong@zhiyong-OptiPlex-7050:~/Desktop/kkk/kkkk$ ll
总用量 35864
drwxrwxr-x 3 zhiyong zhiyong 4096 8月 3 20:14 ./
drwxrwxr-x 3 zhiyong zhiyong 4096 8月 3 20:14 ../
-rw-rw-r-- 1 zhiyong zhiyong 15606298 12月 18 2019 GCF_001442555.1_ACSNU-2.0_protein.faa
-rw-rw-r-- 1 zhiyong zhiyong 21100234 8月 8 2019 GCF_003254395.2_Amel_HAv3.1_protein.faa
2. 进行比对
orthofinder -f path-to-fasta -S method-to-align
-f: 指定蛋白质fasta文件放置的路径
-S: 指定用于比对的方式，包括blast,mmseqs,blast_gz和diamond
3. 结果
3.1 比对结果统计文件
Orthogroups/Orthogroups.GeneCount.tsv
Orthogroup GCF_001442555.1_ACSNU-2.0_protein GCF_003254395.2_Amel_HAv3.1_protein Total
OG0000000 1 50 51
OG0000001 5 42 47
OG0000002 0 46 46
OG0000003 1 43 44
OG0000004 1 37 38
OG0000005 0 38 38
OG0000006 0 36 36
OG0000007 1 34 35
OG0000008 0 33 33
可以根据以上的统计结果来选择
1-to-1的同源基因
3.2 1-to-1同源基因
Orthogroups/Orthogroups_SingleCopyOrthologues.txt
这个文件中给出了所有
1-to-1同源基因所在的orthologous group
3.3 各个orthologous group所包含的各个物种的translation-ID
(base) zhiyong@zhiyong-OptiPlex-7050:~/Desktop/kkk/kkkk/OrthoFinder/Results_Aug03/Orthogroups$ cat Orthogroups.tsv|head -2
Orthogroup GCF_001442555.1_ACSNU-2.0_protein GCF_003254395.2_Amel_HAv3.1_protein
OG0000000 XP_028519937.1 XP_026294641.1, XP_026294642.1, XP_026294643.1, XP_026294644.1, XP_026294645.1, XP_026294646.1, XP_026294647.1, XP_026294648.1, XP_026294649.1, XP_026294650.1, XP_026294651.1, XP_026294652.1, XP_026294653.1, XP_026294654.1, XP_026294655.1, XP_026294656.1, XP_026294657.1, XP_026294658.1, XP_026294659.1, XP_026294660.1, XP_026294661.1, XP_026294662.1, XP_026294663.1, XP_026294664.1, XP_026294665.1, XP_026294666.1, XP_026294667.1, XP_026294668.1, XP_026294669.1, XP_026294670.1, XP_026294671.1, XP_026294672.1, XP_026294673.1, XP_026294674.1, XP_026294675.1, XP_026294676.1, XP_026294677.1, XP_026294678.1, XP_026294679.1, XP_026294680.1, XP_026294681.1, XP_026294682.1, XP_026294683.1, XP_026294684.1, XP_026294685.1, XP_026294686.1, XP_026294687.1, XP_026294688.1, XP_026294689.1, XP_026294690.1
