file1:
string11   seq33
string123  seq334
string12   seq32

file2:
>string11
AGCTAGCTG
CAGAGTC
>string123
AGCTGAAGA
>string12
AGCGATTATCGA
AGCATGAAGACC
ACAGCATGACTA

file3:
>seq32
AGAAGCTCCTAGCT
>seq334
AGCTGAAGA
AAAGCTAGA
>seq33
AGGATTCGA
AAATATGA


my program:
open(FILE1,"file1.txt");
open(FILE2,"file2.txt")
open(FILE3,"file3.txt")
@ray1=<FILE2>;$join1=("",@ray1);@list1=split(">",$join1);
@ray2=<FILE3>;$join2=("",@ray1);@list2=split(">",$join2);
while($s=<FILE1>){
  ($one,$two)=split("\s+",$s);
  @first=grep($one,@ray1);
  @second=grep($two,@ray2);
  #<ACTION - CALLING SUBROUTINE>
  #i should have only 2 sequences here for every loop.
}