Standalone BLAST results

[daniellaplummer]

Hi,

I used to standalone BLAST to subtract the Clostridium difficile proteome from the human proteome, using the command
>blastp -db Human -in Mybacteria.fas -out results.fas -evalue 1e-3 -outfmt 4
The results showed the query hits where the Clostridiums proteome matched the humans, I now need to subtract these matched sequences from the whole clostridium proteome and wondered if there was a quicker efficient way of doing this.
Also if there was is a website that showed how to analyse the results.

Many thanks,

Dani

[colindaven]

You probably need to write a script to do this. Biopython might be a good place to look at for an easy way to parse fasta files.

[Zapages]

if you output your blast results in tabular format then you could try the following.

In terminal try the following:

grep -w Clostridiums input_file > output_file1

grep -w proteome output_file1 > final_output_file

Hope this help.