[Bioperl-l] Fishing redundant sequences in FASTA files [Right formatting]

[Juan Jovel]

Good Morning guys,
> sorry for the naive question: What's the simplest way to fish redundant sequences (complete or partial) between two (or more) fasta files.
> I was thinking just to do it with SeqIO, opening two files, and compare each sequence of file_1 to each record of file_2, like:
# Read each record of file 1 and compare to each read of
file 2

while(my $dna1 = $seqin1->next_seq){

        my $seq1 =
$dna1->seq;

        my $id1 =
$dna1->id;

 

        # Iterate
inside de second fasta file

        while(my $dna2
= $seqin2->next_seq){

                my $seq2 = $dna2->seq;

                my
$id2 = $dna2->id;

 

               
if(($seq1 =~ /$seq2/)||($seq2 =~ /$seq1/)){

                       
print "Match found \n";

                       
print OUT "Records $id1 and $id2 are redundants";

I am afraid it is going to be slow for large files.  AND, more importantly, how do I reset the object containing the second file to the first line, as done in Perl with (SEEK(IN, 0,0)) for example.  Does SeqIO allows that (sorry, I am not a frequent user of SeqIO). If there is another more-elaborated module to fish such redundant sequences, I will appreciate to know.

Thanks,
JUAN