How can I run All-v-all BLAST
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
1 answer
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.
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Command line options for blast can be found here and a comprehensive command line blast manual is here.
And this OrthoMCL practical guide.
Tank you, I am going to read right now.