How do I blast a local query against a local database?

Question

[ivanabarbona]

I have my own query (multifasta) and database (multifasta) but I don't know the specific comands to perform blast locally. I'm trying to do this directly from the comand prompt in Ubuntu 13.04. I also have tried doing this through Blast Perl Api but it doesn't work either.

Thanks in advance.

Ivana

Answer 1

[Pierre Lindenbaum]

"BLAST Command Line Applications User Manual" http://www.ncbi.nlm.nih.gov/books/NBK1763/

[ivanabarbona]

Thaks for your answer. We have been working with the manual for installation and configuration, but our goal is to run blast with our own query and database. These multi fasta files are not downloaded from NCBI. That is why it gets difficult for us to do it. We would really appreciate your help.

[Pierre Lindenbaum]

In the manual

(...) Makeblastdb can be invoked for this file as below.

$ makeblastdb -in mydb.fsa -parse_seqids -dbtype nucl