Bioinformatics for Biologist: Installing standalone BLAST+ on linux

I'm sure most of us use NCBI blast on a daily basis. I use blast2sequences frequently. Sometimes I get frustrated because I cannot blast two set of sequences to each other. This leads me to explore options on how to run a local blast.

So what is standalone BLAST? The answer below is quoted from NCBI faq section:

"The StandAlone WWW BLAST Server allows you to set up your own in-house version of the NCBI BLAST Web pages. This can be accessed through web browsers on intranet web servers. You can set up the program to search your own custom databases or downloaded copies of the NCBI databases. The StandAlone WWW BLAST Server is available by anonymous FTP at ftp://ftp.ncbi.nih.gov/blast/server/current_release/."

Free software such as Bio-edit can perform local blast. Unfortunately, it cannot handle a huge amount of data and it only run on Windows. Another alternative is BLAT. Some people align short reads to genome using BLAT due to its speed.

The advantage of running a standalone BLAST is you can use the blast algorithm to search for your queries against the database you created (aka local blast). Your database can be a nucleotide or peptide FASTA file of your data or any data downloaded online.


The latest edition is BLAST+, an improved version of BLAST. The tar file can be downloaded from ftp://ftp.ncbi.nih.gov/blast/executables/. After untar, you will get the ncbi-blast folder with two folders inside: bin and doc. The commands:

>cd ncbi-blast-2.2.23+/bin/
#cd to where the blast executables are
>./makeblastdb -in database1.fa -dbtype nucl -out database1
#make the local database. Three files with extension .nrh, .nin and .nsq will be produced.
>./blastn -help # for more options
>./blastn -task blastn -db database1 -query query1.fa -out results1.txt -evalue 1E-50 -outfmt 6
#run blastn with blastn algorithm. Just type in database name, query file, output name and you can even select the E-value. Output format 6 presents results in table form.


Done!