just install bioperl and use the module Bio::SeqIO to read in this FASTA format ... like this. Note that I haven't tested it.. but it should work in this fashion. 
use strict; # you do use strict don't you?
use Bio::SeqIO;
# your file containing the patterns
open (INP,"data.txt") || die "cant find it!"; 

while (my $line = <INP>) {
  chomp $line;
  # separate pattern from filename
  my ($filename,$pattern) = split (/\s+/,$line);

  #open the file that should be searched
  my $seqio_object = Bio::SeqIO->new(-file => $filename, -format=>"fas
+ta");

  #loop through all the fasta sequences
  while ($seq_object = $seqio_object->next_seq){
     my $sequence = $seq_object->seq;
     my $id = $seq_object->display_id;     
    #check if pattern exists
    if ($sequence =~ /$pattern/g) {
       print "$pattern found in $id in file $filename\n";
     }
  }

}

[download]
However, on another note, its probably better to post Bioperl questions on the bioperl mailing list. Google for it.

----------------------

"with perl on my side"

In reply to Re: grep the whole element in an array by perliff
in thread grep the whole element in an array by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.