Ok, a more detailed hint:
1: read the motif file using Bio::SeqIO, and store those motif in a hash.
2: traverse through the target sequence file usingBio::SeqIO. On each target seq, use index on each motif to find whether the seq has the motif.
use strict;
use Bio::SeqIO;

my $file_seq = shift;
my $file_motif = shift;

# read all motif
# store in hash: ID => motif_seq
my %all_motif;

my $MOTIF_FH = Bio::SeqIO->new(-file=>$file_motif);
while (my $obj = $MOTIF_FH->next_seq) {
  $all_motif{$obj->display_id} = $obj->seq;
}
$MOTIF_FH->close;

# traverse through all sequences
my $SEQ_FH = Bio::SeqIO->new(-file=>$file_seq);

while (my $obj = $SEQ_FH->next_seq) {
  my $id  = $obj->display_id;
  my $seq = $obj->seq;

  print "Sequence: $id\n";
  
  # traverse through all motifs
  foreach my $motif_id (sort keys %all_motif) {
    my @curr_result;
    
    # find all positions of current motif
    my $last_i = 0;
    while (1) {
      my $i = index($seq,$all_motif{$motif_id},$last_i);
      last if $i==-1;
      push @curr_result,$i+1;
      $last_i = $i;
    }
    
    # print if has result
    if (@curr_result>0) {
      print "\tmatch with $motif_id at: @curr_result\n";
    }
  }
}

$SEQ_FH->close;

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In reply to Re: How to find any of many motifs? by llancet
in thread How to find any of many motifs? by Nikulina

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