BioPHP - Sequence to pattern

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

Transforms a DNA sequence into a pattern
Example: from RCGY to [AG]CG[CT]

Code

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

function seq_to_pattern_with_UIB($seq) {
        $seq=preg_replace("/N/",".",$seq);
        $seq=preg_replace("/Y/","[CT]",$seq);
        $seq=preg_replace("/R/","[AG]",$seq);
        $seq=preg_replace("/W/","[AT]",$seq);
        $seq=preg_replace("/S/","[CG]",$seq);
        $seq=preg_replace("/K/","[GT]",$seq);
        $seq=preg_replace("/M/","[AC]",$seq);
        $seq=preg_replace("/D/","[AGT]",$seq);
        $seq=preg_replace("/V/","[ACG]",$seq);
        $seq=preg_replace("/H/","[ACT]",$seq);
        $seq=preg_replace("/B/","[CGT]",$seq);
return ($seq);
}