Perhaps you can clarify your question a bit. As I read it, there are at least two possible meanings: Are you seeking:

1. help on how to read a file in fasta format into your program?
   or
2. suggestions about where to "read into" (in the British sense of the phrase) the fasta format?
   I think the generic English for the latter would be: "read about the fasta format;" "study the fasta format" or similar).

http://bioinformaticsweb.net/tutorial.html may lead you to answers on either. Or, perhaps, one of the bio-monks will happen by and have a better idea, but in the meantime, you may wish to use Super Search with fasta, bioinformatics or bioperl as a search term. Here's a small sample of what's available here.

Read Perl and Bioinformatics in a welcoming note to you..

Now, a FastA file is just a string representing a nucleotide (DNA|RNA) sequence or a Protein sequence, Perl has different strong string manipulation approaches, you can access such a file format either directly (for input or output), check File Input and Output in the Tutorials or you can use one of the BioPerl modules to get an object that includes this file and which you can process further.

The best thing in BioPerl is that you don't have to worry about implementing parsing measures if the file format is recognized by the module you would use and that there is support for many formats (ex. Genbank, FastA...etc), you can even convert among these formats or generate a sequence from scratch in a particular format all the way through to very advanced bioinformatics tasks that involve sequence analysis.. The possibilities are just abound..

Here is a quick example to create an input sequence object and do a basic analysis..

use strict;
use warnings;

#counting motifs

use Bio::SeqIO;
my $file = "SeqHisham.txt";
my $in = Bio::SeqIO->new(
        -format =>'fasta',
        -file   =>$file,
        );
my $motif_Count=0;
my $motif = 'ga';
while(my $seq = $in->next_seq){
        #since the sequence would be processed in a certain way conver
+t to string
        my $string = $seq->seq;
        if($string=~/$motif/i){ #make the regex appropriate...
                $motif_Count++;
                }
        }
print "Found $motif_Count hits\n";
[download]

Best of luck and have a nice Perl journey

probably a solved problem