BioPHP - PHP Bioinformatics class

BioPHP is an easy to use, open source project. BioPHP implements a selection of simple tools for manipulating genomic data. We're not doing any heavy lifting here (this is PHP). This class is built for basic RNA, DNA, and Protein manipulation.

Simple Usage:

Find Reverse Complement

$BioPHP = new BioPHP('ATGAAA');
$BioPHP->reverseSequence(); //reverse sequence
$BioPHP->complementDnaSequence(); //get the reversed complement
echo $BioPHP->sequenceA;
//prints TTTCAT

Calculate GC Content

$BioPHP = new BioPHP('ATGAAAGCATC');
echo $BioPHP->gcContent();
//prints 36.3636

Count Point Mutations Between Two Sequences

$BioPHP = new BioPHP('CTGATGATGGGAGGAAATTTCA','CTGATGATGCGAGGGAATATCG');
echo $BioPHP->countPointMutations();
//prints 4

Translate DNA Sequence to Amino Acid Sequence

$BioPHP = new BioPHP('CTGATGATGGGAGGAAATTTCAGA');
echo $BioPHP->translateDna();
//prints LMMGGNFR

Calculate Monoisotopic Mass

$BioPHP = new BioPHP('CTGATGATGGGAGGAAATTTCAGA');
$proteinSequence = $BioPHP->translateDna()."\n"; //translate sequence
echo $BioPHP->calcMonoIsotopicMass($proteinSequence)."\n"; //calculate mass
//prints 906.42041

Finding a Motif in DNA

$BioPHP = new BioPHP('ATAT', 'GTATATCTATATGGCCATAT');
echo $BioPHP->findMotifDNA();
//prints 3 9 17

Get Reading Frames

$BioPHP = new BioPHP('GTATATCTATATGGCCATAT');
print_r( $BioPHP->getReadingFrames() );

/*
* returns array containing...
Array
(
    [0] => GTATATCTATATGGCCATAT
    [1] => TATATCTATATGGCCATAT
    [2] => ATATCTATATGGCCATAT
)
*/

//Protip: To get all 6 reading frames. Use the reverse and complement methods, then pass the result to getReadingFrames()

Find most common likely ancestor

$fastaSequence = "
>Sequence 1
ATCCAGCT
>Sequence 2
GGGCAACT
>Sequence 3
ATGGATCT
";

$BioPHP = new BioPHP();
$fastaArray = $BioPHP->readFasta($fastaSequence); //read and parse the sequences
echo $BioPHP->mostLikelyCommonAncestor($fastaArray)."\n";

//prints ATGCAACT

Get a fasta result from Uniprot and calculate isotpoic mass

$BioPHP = new BioPHP();
$uniprotFasta =  $BioPHP->getUniprotFastaByID("B5ZC00"); //returns the result from Uniprot as a string
$fastaArray = $BioPHP->readFasta($uniprotFasta); //parses the response
echo $BioPHP->calcMonoIsotopicMass($fastaArray[1]['sequence'])."\n";

//prints 55319.0636