Raj at 18:42, 5 January 2010

2010-01-05T18:42:00Z

← Older revision		Revision as of 18:42, 5 January 2010
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	Category:Bioinformatics		[[Category:Bioinformatics]]

	* Blast		* Blast

Raj: Created page with 'Category:Bioinformatics * Blast ** Install the source and compile it ** Format database

 # Variables 	my $path    = "/home/raj/bio"; 	my $dbdir   = "$path/tobacco/data/bla…'

2010-01-05T18:41:26Z

Created page with 'Category:Bioinformatics * Blast ** Install the source and compile it ** Format database <pre> # Variables my $path = "/home/raj/bio"; my $dbdir = "$path/tobacco/data/bla…'

New page

Category:Bioinformatics

* Blast
** Install the source and compile it
** Format database
<pre>
# Variables
my $path = "/home/raj/bio";
my $dbdir = "$path/tobacco/data/blastdb";
my $db = "$dbdir/tgi_singlet";
my $infile = "$path/tobacco/data/tgi_singlet.fa";

# Formatting
chdir $dbdir;
`formatdb -i $infile -p F -n $db`;
<pre>
** Run Blast
<pre>
Variables
my $path = "/home/raj/bio";
my $db = "$path/tobacco/data/blastdb/tgi_singlet";
my $query = "$path/tobacco/blast/tilling/tilling_genes.fa";
my $outfile = "$path/tobacco/blast/tilling/tilling_genes.blast.out";
my $cpu = "4";

Programe

`blastall -p blastn -d $db -i $query -e 1 -m 9 -q -5 -v 1 -o $outfile -a $cpu`;
# -p program
# -d database
# -i query file
# -e evalue
# -m 8 tab delimited out
# -o outfile
# -a number of CPUs
# -q Penalty for a nucleotide mismatch (blastn only) default = -3
# -v Number of database sequences to show one-line
# -K Number of best hits from a region to keep
</pre>

Blast - Revision history

Raj at 18:42, 5 January 2010

Raj: Created page with 'Category:Bioinformatics * Blast Install the source and compile it Format database
# Variables my $path = "/home/raj/bio"; my $dbdir = "$path/tobacco/data/bla…'