BioPHP - PHP Bioinformatics class

BioPHP is an easy to use open source project. BioPHP implements a selection of simple tools for manipulating genomic data. PHP 7 has benchmarked much faster than Python, this class aims to build tools for basic RNA, DNA, and Protein manipulation. Future plans include creating an experimental de novo assembly tool, and online project portal.

Simple Usage:

Find Reverse Complement

$BioPHP = new \kap\BioPHP();
$result = $BioPHP->reverseSequence('ATGAAAGCATC');
$result = $BioPHP->complementDnaSequence($result);
//prints TTTCAT

Calculate GC Content

$BioPHP = new \kap\BioPHP();
echo $BioPHP->gcContent('ATGAAAGCATC', 4)."\n";
//prints 36.3636

Count Point Mutations Between Two Sequences

$BioPHP = new \kap\BioPHP();
echo $BioPHP->countPointMutations('CTGATGATGGGAGGAAATTTCA','CTGATGATGCGAGGGAATATCG')."\n";
//prints 4

Translate DNA Sequence to Amino Acid Sequence

$BioPHP = new \kap\BioPHP();
echo $BioPHP->translateDna('CTGATGATGGGAGGAAATTTCAGA')."\n";
//prints LMMGGNFR

Calculate Monoisotopic Mass

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

Finding a Motif in DNA

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

Get Reading Frames

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

/*
* 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 \kap\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 \kap\BioPHP();
$uniprotFasta =  $BioPHP->getUniprotFastaByID("B5ZC00"); //returns the result from Uniprot as a string
$fastaArray = $BioPHP->readFasta($uniprotFasta); //parses the response
echo $BioPHP->calcMonoIsotopicMass($fastaArray[0]['sequence'])."\n";

//prints 55319.0636

Find Protein Motif using a variable "shorthand" motif search

$BioPHP = new \kap\BioPHP();
$results = $BioPHP->findMotifProtein("N{P}[ST]{P}","B5ZC00");
print_r($results);

/*
* returns array containing...
Array
(
    [0] => 85
    [1] => 118
    [2] => 142
    [3] => 306
    [4] => 395
)
*/

//Notes: The second parameter expects a protein access ID string used to lookup the full sequence via UniProt.

Finding a shared motif

This task can be very CPU intensive. Using PHP 7, this method benchmarked faster than Python! Runtime results were about 1 second with a collection of 100 DNA strings of length 1 kbp each.

$fasta="
>Sequence 1
GATTACA
>Sequence 2
TAGACCA
>Sequence 3
ATACA";

$BioPHP = new \kap\BioPHP();
$fastaArray = $BioPHP->readFasta($fasta);
$result = $BioPHP->findLongestSharedMotif($fastaArray);
echo $result."\n";
//prints TA

Find open reading frames from DNA Sequnce

$sequence = ">Test DNA Sequence
TCCCCGGACTCCAAACGCTCGGTAGCCGCCCCTGCTCGACATATTTAGCTCCCTGCATTG
ACGCCCTGGCAGCCCCGATCAATTTTCGTGGTTAAACGCGCGCTCGCAAGGGACATCGAC
CGGACCACAGAGCATAGCATGCCTTAGGATCGCCTGTCACTGTTCGTCTCCCTATTTGAG
CACTGTAGCCCCTGGTACCCCCGTCCTGAAGCGTGTGTGATACACGGTCTGCCCAAGATG
";

$BioPHP = new BioPHP();
$results = $BioPHP->printORFProteins($sequence);
print_r($results);

/*
* Returns the following array
Array
(
    [0] => MP
    [1] => MLCGPVDVPCERAFNHEN
    [2] => MLCSVVRSMSLASARLTTKIDRGCQGVNAGS
    [3] => MSLASARLTTKIDRGCQGVNAGS
)

*/