How to blast mutiple sequences to local database?

Question

[tmms]

Dear all

I am fairly new to using blast, especially at the command line. In the nex paragraph, I will sketch my problem.

I have two files with sequences (formated as a fasta-file: >header \n sequence ...). I already translated them into proteins. I already made a local database of one of the files with the "makeblastdb" command. Now I would like to blast (blastp) every sequence from the other file to that database, but I have no idea how to do this. In the manual (Blast+) I could not find an answer.

Thanks in advance.

Answer 1

[st.ph.n]

/path/to/blastp -query /path/to/inputfile.fasta -db /path/to/dbfile.fasta -num_threads N -outfmt 6 -out blastp.out.txt

where: -query is your fasta that you're blasting -db is the name of the database from makeblastdb -num_threads is the number of processors to use -outfmt 6 is tab-delimited output (my preference for parsing later) See here for other options. -out is the name of the output file

Use /path/to/blastp -h for more options.