[Bioperl-l] which one and how to configure(blastall)

[Stefan Wächter]

Hi Yanfeng,

Try this:
(I make the assumption, that your blast installation is in 
/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10).
 
Create a file named   .ncbirc (don't forget the little dot)  in 
/home/yanfeng and write the following in this file:

    [NCBI]
    DATA="/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10/data"

save file.

In the data dir, BLAST will find the BLOSSUM tables.

In your blast installation dir you will find also db dir. That's a good 
place to store your blast databases.

Set the environment variables in your .bashrc  (.profile, .cshrc...... - 
depends on your shell) . I know it's trivial, but..... .

something like [bash]:

<>BLASTDIR=/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10
<>export BLASTDIR

<>BLASTDB=/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10/db
<>export BLASTDB


Additionally it is an good idea to add 
/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10 in your PATH variabel.
 

In a last step you have to install one of the NCBI databases in the 
BLASTDB dir or create one with formatdb

Hope I could help

Cheers
Stefan


yanfeng wrote:

> Hi, Sorry to bother you again.
> I want to download blast program now
> I want to run blast and get blast report.
> I donot know which one I should install and how to configure it( is 
> that  like " export BLASTDIR=/ data1/blast/ " )
> I use
> BEGIN {
> $ENV{'BLASTDIR'} = 
> '/home/yanfeng/blast-2.2.10-amd64-linux/blast-2.2.10/';
> }
>
> but it doesnot work.
>
> blast-2.2.10-amd64-linux.tar.gz 
> <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.10/blast-2.2.10-amd64-linux.tar.gz> 
>
> blast-2.2.10-ia32-linux.tar.gz 
> <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.10/blast-2.2.10-ia32-linux.tar.gz> 
>
> blast-2.2.10-ia64-linux.tar.gz 
> <ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.10/blast-2.2.10-ia64-linux.tar.gz> 
>
>
>
> My perl script
> //
> use Bio::SeqIO;
> use Bio::Seq;
> use Bio::Tools::Run::StandAloneBlast;
> $seqio_obj = Bio::SeqIO->new(-file => 'mun_lab.fasta',
>                           -format => 'fasta' ); # to wrtie the 
> sequence to afasta file
> $seq_obj = $seqio_obj->next_seq;
> #print $seq_obj->seq,"\n";
> @params = (program  => 'blastn',
>         database => 'db.fa' );
> $blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
> $report_obj = $blast_obj->blastall($seq_obj);
> $result_obj = $report_obj->next_result;
> print $result_obj->num_hits;
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