This is a site about programming with Perl. As such, the best questions tend to be technical in nature, provide a bit of sample input, some sample output, and 10-30 lines of code demonstrating the problem. We will not be able to help you without actually seeing the part of the script that you are having trouble with.

Welcome, your previous post provided some advice with regards asking for help, it would be a more productive use of your time to pay attention to this. Not everyone works with bioinformatics, the advice given in your cross post to biostars suggests using Bio::DB::Fasta, part of the BioPerl suite. Perhaps this will suffice, otherwise you'll have to learn some Perl to alter the script you have to do what you want, or write a shell script or batch file to automate feeding your list of sequences to the program.

Does your script start like this and have 700+ lines ?

#!/gpsr/local/bin/perl
use Getopt::Std;
getopts('i:o:');
$infile=$opt_i;
$outfile=$opt_o;

if($infile eq "" or $outfile eq "")
{
        print "\t./algpred.pl -i input_file -o output_file\n\n";
        print "\t-i:\tinput file in fasta format\n";
        print "\t-o:\toutput file\n";
        print "\n\tExample: ./algpred.pl -i /gpsr/examples/example.fas
+ta -o out.algpred\n";
        exit;
}
$ptnnum = `grep -c "^>" $infile`; chomp($ptnnum);
if($ptnnum > 1)
{
        print "\tDon't Enter multiple sequences... Enter single sequen
+ce fasta file\n";
        exit;
}
[download]

Are you asking how to run this script many times using a different inputfile each time ?