Question: How to fetch sequences from Proteinortho5 output containing all test species and no duplication in each genome
0
gravatar for saadleeshehreen
14 months ago by
saadleeshehreen70 wrote:

Hi, I want to construct a phylogenic tree on 100 Pseudomonas aeruginosa genomes. Before constructing the tree, I want to first cluster those genomes on the basis of homology and for this purpose, I am using ProteinOrtho5 software. After running the software with synteny option I want to extract protein sequences from the output those only containing all test species and no duplication in each genome. I understand I need to run grab_protein.pl on myproject.poff to do this but how can customize/filter the output before running grab_protein.pl? I followed as following proteinOrtho out put help required But grep '^4\t4' output.proteinortho didn't print anything for me. As I tested the software on 3 species, I modified it from 3 to 4. Anyone help about the filtering? Cheers

proteinortho5 • 393 views
ADD COMMENTlink modified 8 months ago by AlishaQ0 • written 14 months ago by saadleeshehreen70
0
gravatar for h.mon
14 months ago by
h.mon29k
Brazil
h.mon29k wrote:

If you run on three species, your command should be:

grep '^3\t3' output.proteinortho
ADD COMMENTlink written 14 months ago by h.mon29k
0
gravatar for AlishaQ
8 months ago by
AlishaQ0
AlishaQ0 wrote:

grep $'^3\t3' output.proteinortho

ADD COMMENTlink written 8 months ago by AlishaQ0

My flavor of Linux required the $ character in front - yours might too.

ADD REPLYlink written 7 months ago by AlishaQ0
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