A Genbank file is made of a series of Genbank records separated by a line consisting of "//"

You are reading your file line by line:  while ($line = <$IN>) and splitting each line in different lines (??) my @line = split(/\///,$line). Obviously, this is not what you want.

An easy way to solve this is to read the file record by record by assigning the value "//" to $/ (see perlvar) and then process the record

Another possibility is to read the file line by line, and update the $accession, $biotype and $sequence variables, accordingly. But you can be in a problem if a record doesn't have one of them

Update: Following the first approach:

use strict;
use warnings;

$/ = "//";

my $genfile = "c:\bemisia_coi.gb";
open my $ifh, "<", $genfile or die "cannot open $genfile: $!\n";

while (my $chunk = <$ifh>){
  last if eof $ifh;
  my ($accession) = $chunk =~ /LOCUS\s*([A-Z]*\d+)/;
  my ($biotype) = $chunk =~ /BIOTYPE\s*([A-Z])/;
  my ($sequence) = $chunk =~ /ORIGIN\s*(.*)$/s;
  $sequence =~ s/\s|\d//g;
  my $outfile = "${accession}_${biotype}";
  open my $ofh, '>' $outfile or die "cannot open $outfile: $!\n";
  print $ofh, ">$accession\n$sequence";
  close $ofh;
}
[download]

Additional comments:

• You don't need to lc your input
• I've never seen a "biotype" field in a Genbank file (I can't find it in the specs either), but I may be wrong, so I conserved the code that tries to capture that field, instead you can see the molecule type in the LOCUS field (DNA|PROT)
• A typical "locus name" is made of letters (2 or 3) and numbers, you only test for 8 letters
• The last record of the file is always empty (because the file ends with a "//") line, that is why I use last if eof $ifh;
• Don't forget to close each output file when it is not needed, a Genbank file could be very large and you can run out of open filehandles, they are a finite resource on every operating system
• The "ORIGIN" sub-record is multi-line, so you should add the /s modifier to your regexp (see perlre)
• If you want to scape the "//" in a regular expression, you should escape both slashes: /\/\//
• $sequence =~ s/\s//g; $sequence =~ s/\d//g; can be written $sequence =~ s/\s|\d//g;

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