This looks like a multi-fasta file holding DNA or protein sequence data (with sequence ID after the >). I use one of the following two ways to get this info into an array before piping into blast or other sequence manipulations. The first is a loop from some hand-me-down code that works quite well (but any comments etc on optimization etc v. welcome...) 
open( FASTAFILE, $ARGV[0] );
while (<FASTAFILE>) {

    if ( /^>/ && $seqflag == 1 ) {
        push ( @sequences, $fasta );
        $fasta = "";
        $fasta = $_;

    }
    elsif (/^>/) {

        $fasta   = $_;
        $seqflag = 1;

    }
    else {

        $fasta .= $_;

    }
}

push ( @sequences, $fasta );
#then iterate @sequences to run over BLAST

[download]
The other (better?) way is the very nice Bioperl modules that have methods that specifically handle multifasta flat files. Also check out EMBOSS, a sequence analysis suite that interfaces with BioPerl...EMBOSS + BioPerl makes life sooo much easier... From the bioperl tutorial... 
  # script 1: create the index
  use Bio::Index::Fasta; # using fasta file format
  $Index_File_Name = shift;
  $inx = Bio::Index::Fasta->new(
      -filename => $Index_File_Name,
      -write_flag => 1);
  $inx->make_index(@ARGV);

  # script 2: retrieve some files
  use Bio::Index::Fasta;
  $Index_File_Name = shift;
  $inx = Bio::Index::Fasta->new($Index_File_Name);
  foreach  $id (@ARGV) {
      $seq = $inx->fetch($id);  # Returns Bio::Seq object
      # do something with the sequence
  }

[download]
Hope this helps,

tandemrepeat

In reply to Re: writing to arrays by tandemrepeat
in thread writing to arrays by Superman

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