Localization (BLAST 2.2.29+) under the Linux BLAST +

Links: http://blog.sciencenet.cn/home.php?mod=space&uid=830496&do=blog&quickforward=1&id=640600

 

Linux localization of the BLAST + (NCBI-BLAST 2.2.29+):

1. Download the software BLAST:

   At the following URL   ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ 

   Download: ncbi-blast-2.2.29 + -x64-linux.tar.gz (according to their choice of operating systems).

 

2. Extract:

    Placed at any directory can be unpacked, the corresponding path is added to the PATH variable.

    For example to extract the user's home directory (/ home / yonpen) next, after extracting the file folder rename BLAST, BLAST all the programs in the directory + / home / yonpen / blast / bin.

 

3. Add the environment variable:

Open the terminal (Terminal), switch to the root user, execute vim / etc / profile (basic need to know that Vim editor).

At the end of the most added:

export PATH=/home/yonpen/blast/bin:$PATH

Save and exit. (Determined by the value of the environment variable path Blast lies.)

If successful here, blastn -version displays the version information (be sure to log off or restart the computer) after cancellation of execution.

 

4. New:

Create a new folder in the directory / home / yonpen / blast, named db.

Create a new file in the / home / yonpen, named .ncbirc. (File name begins with a dot)

Add the contents of the file:

[BLAST]

BLASTDB=/home/yonpen/blast/db

 

5. Download FASTA format database:

 ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/

Such as downloading nr.gz.

 

6. Establish BLAST + available databases:

 Open the terminal (Terminal), switching to the next / home / yonpen / blast / db directory is performed (Case nr database of protein):

makeblastdb  –in nr  -parse_seqids  -hash_index  -dbtype prot  

(Needs its own input, line copy command may not work, do not know why)

 

7. Use program:

Such as the use psiblast

In the directory / home / yonpen / blast new three folders, named pssm, input, output

File name where the query sequence to be set up for a.fasta (a file put a sequence and must be fasta format)

Excuting an order:

psiblast  -comp_based_stats 1  -evalue 0.001  -num_iterations 3  -db nr   -query input/a.fasta  -out output/a.txt  -out_ascii_pssm pssm/a.pssm