BioPHP - Find palindromic sequences

Original code submitted by joseba
Code bellow is covered by GNU GPL v2 license.

Description

Last change: 2010/10/18 17:04 | Edit description | Recent Changes | Original description

Searches for palindromic sequences within a DNA sequence.
Length of palindromic sequences to be searched will be between $min and
$max values
Will return an array with key = start position and val= palindromic
sequence

Requires function DNA_is_palindrome

Code

Last change: 2010/10/18 17:04 | Edit Code | Recent Changes | Download | Original code

function find_palindromic_seqs ($seq,$min, $max){
   $result="";
   $seq_len=strlen($seq);
   for($i=0;$i<$seq_len-$min+1;$i++){
      $j=$min;
      while($j<$max+1 and ($i+$j)<=$seq_len){
      if (is_odd($j)==1){$j++;continue;}
      $sub_seq=substr($seq,$i,$j);
      if (DNA_is_palindrome($sub_seq)==1){
      $results [$i]=$sub_seq;
      }
      $j++;
      }

   }
   return $results;
}