Info | Home

BioPHP - Reverse-Complement of DNA 2

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

This function is derived from RevComp_DNA function. I think it may be
interesting to maintaing RevComp_DNA and RevComp_DNA2 as two separated
functions; for
big sequences, the functions may be selected depending on needs.

This function allows transforming the sequence when degenerated
nucleotides are present.

Code

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

function RevComp_DNA2($seq){
 $seq= strtoupper($seq);
 $seq=strrev($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);
 $seq= strtoupper ($seq);
 return $seq;
}