BioPHP - Nucleotide composition

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

Calculates nucleotide composition of sequences.

Code

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

function nucleotide_composition ($seq) {
        $seq=strtoupper($seq);
        $result["A"]=substr_count($seq,"A");
        $result["C"]=substr_count($seq,"C");
        $result["G"]=substr_count($seq,"G");
        $result["T"]=substr_count($seq,"T");
        $result["Y"]=substr_count($seq,"Y");
        $result["R"]=substr_count($seq,"R");
        $result["W"]=substr_count($seq,"W");
        $result["S"]=substr_count($seq,"S");
        $result["K"]=substr_count($seq,"K");
        $result["M"]=substr_count($seq,"M");
        $result["D"]=substr_count($seq,"D");
        $result["V"]=substr_count($seq,"V");
        $result["H"]=substr_count($seq,"H");
        $result["B"]=substr_count($seq,"B");
        $result["N"]=substr_count($seq,"N")+substr_count($seq,"X")+;
        // print_r($result);
        return $result;
}