Blast

Category:Bioinformatics

• Blast
  • Install the source and compile it
  • Format database

# 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