Question: How can I run All-v-all BLAST
2
gravatar for Esaie
3.4 years ago by
Esaie110
Canada
Esaie110 wrote:

Hello, I order to run completely orthoMCL, i must run All-v-all BLAST on my goodProteins.fasta file, but I dont understand very well how to run it by using these paramters -F 'm S' -v 100000 -b 100000 -z protein_database_size -e 1e-5, Can anyone who already done it can help me or give me an commande samples please . Tank you

orthomcl blast all-v-all blast • 2.8k views
ADD COMMENTlink modified 3.4 years ago by ALchEmiXt1.9k • written 3.4 years ago by Esaie110
1

Command line options for blast can be found here and a comprehensive command line blast manual is here.

And this OrthoMCL practical guide.

ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by genomax75k

Tank you, I am going to read right now.

ADD REPLYlink written 3.4 years ago by Esaie110
2
gravatar for ALchEmiXt
3.4 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

Not sure if you need to stick to running orthoMCL for your question. I have really good experience with proteinortho5 (which is also really fast). Its usages is also very simple.

ADD COMMENTlink written 3.4 years ago by ALchEmiXt1.9k

oh my bad. Seems orthoMCL is an ortholog classifier...

ADD REPLYlink written 3.4 years ago by ALchEmiXt1.9k
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