Performs a reverse compliment of a nucleotide sequence.

Parameters

$sequence: The nucelotide sequence.

Return value

an upper-case reverse complemented sequence.

Related topics

File

tripal_chado/api/modules/tripal_chado.feature.api.inc, line 64

Provides API functions specificially for managing feature records in Chado.

Code

function chado_reverse_compliment_sequence($sequence) {

  $seq = strtoupper($sequence);
  $seq = strrev($seq);
  $seq = str_replace("A", "t", $seq);
  $seq = str_replace("T", "a", $seq);
  $seq = str_replace("G", "c", $seq);
  $seq = str_replace("C", "g", $seq);
  $seq = str_replace("Y", "r", $seq);
  $seq = str_replace("R", "y", $seq);
  $seq = str_replace("W", "w", $seq);
  $seq = str_replace("S", "s", $seq);
  $seq = str_replace("K", "m", $seq);
  $seq = str_replace("M", "k", $seq);
  $seq = str_replace("D", "h", $seq);
  $seq = str_replace("V", "b", $seq);
  $seq = str_replace("H", "d", $seq);
  $seq = str_replace("B", "v", $seq);
  return strtoupper($seq);
}