I wrote a Perl programme to exact alignment from blast tab limited out put. it works perfectly for small inputs but while trying with huge data set (more than 4 gb) about 4-5 hour taken to process a data set. I want to extract more than 4000 data sets and its not possible to do with this programme. kindly tel any alternation for this.

Perl programme

use warnings;

print "Enter Your BLAST result file name:\t";
chomp($blast = <STDIN>);
print "\n";

print "Enter Your Gene list file name:\t";
chomp($database = <STDIN>);
print "\n";

open IN,"$blast" or die "Can not open file $blast: $!";

@ids = ();
@seq_start = ();
@seq_end = ();

while(<IN>){
    @feilds = split("\t",$_);
    push(@ids,$feilds[1]);
    push(@seq_start,$feilds[6]);
    push(@seq_end,$feilds[7]);
}
close IN;

open OUT,">Result.fasta" or die "Can not open file $database: $!";

for($i=0;$i<=$#ids;$i++){
    ($sequence)    = &block($ids[$i]);
    ($idline,$sequence) = split("\n",$sequence);
    if($seq_start[$i] <= 100){
        $pos_Start = 0;
    }
    else{
        $pos_Start = $seq_start[$i]-101;
    }

    $pos_end = $seq_end[$i]+100;
    if($pos_end >= length($sequence)){
        $pos_end = length($sequence);
    }

    $seqlen = $pos_end - $pos_Start;
    $Nucleotides = substr($sequence,$pos_Start,$seqlen);
    $Nucleotides =~ s/(.{1,60})/$1\n/gs;

    print OUT "$idline\n";
    print OUT "$Nucleotides\n";
}
print "\nExtraction Completed...";

sub block{
    $id1 =shift;
    print "$id1\n";
    $start = ();

    open IN3,"$database" or die "Can not open file $database: $!";

    $blockseq = "";
    while(<IN3>){
        if (($_ =~ /^>/)&&($start)){
        last;
        }

        if (($_ !~ /^>/)&&($start)){
            chomp;
            $blockseq .= $_;
        }

        if (/^>$id1/){
            $start = $.-1;
            $blockseq .= $_;
        }
    }
close IN3;

return($blockseq);
}