Hello BrowerUk, I really appreicate the feedback, I was doing the wrong thing all along by not looking through the code. i finally figured it out. This was my revised code. Thanks again. 

#!/usr/bin/perl -w

use strict;




my $filename;
my $accession_id;
my %accession;
my $gene_Name;

print "Please enter in the filename: ";
chomp($filename = <STDIN>);

print "Please enter in the accession_ID: ";
chomp($accession_id = <STDIN>);

open(FILENAME, $filename) or die "cannot open file: $! ";
while($_ = <FILENAME>) {
if ($_ =~ />gi/) {
$gene_Name = $_;
}
else {
}
  $accession{$gene_Name} .= $_;

}

foreach $gene_Name (keys %accession) {
 if ($gene_Name =~ /$accession_id/i) {

print "$accession{$gene_Name}\n";
}

}

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In reply to Re^2: fasta file by PrincePerl
in thread fasta file by PrincePerl

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