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

Calculate GC Content

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

Count Point Mutations Between Two Sequences

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

Translate DNA Sequence to Amino Acid Sequence

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

Calculate Monoisotopic Mass

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

Finding a Motif in DNA

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

Get Reading Frames

$BioPHP = new 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 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[0]['sequence'])."\n";

//prints 55319.0636

Find protein motif using a variable "shorthand" motif search

$BioPHP = new 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 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
)

*/

Locating restriction sites between length of 4 and 12

$BioPHP = new BioPHP();
$results = $BioPHP->findRestrictionSites("TCAATGCATGCGGGTCTATATGCAT", 4, 12);
//returns an array containing postion and length of restrictions

Inferring mRNA from Protein - calculates total different RNA strings from which the protein can be translated

Note: This method requires the use of the PHP Math Big Integer package which is a composer dependency of this project.

$BioPHP = new BioPHP();
$result = $BioPHP->inferringMRnaFromProteinCount("MTIFMFHNKNICTEYMGYYDQQIMQTEHKWYWDFHTFMIPNVFYEDVIKFKMRMLMIPNCFFGPWLFCKLEKCQYYEKATEPAPIVKDYTLFATGGAGREATFWPWFWTDENRPKDYYFQRDGLHHRNEPRLPHATCRRAYYQCEMIQYAIVTSCVLLAWKMFTDYGHTGVASEPKEPQEDIKCMKFPHMSWQKTLTEAFYELFPCYPEEFPNDRPWLLGHGFGPIVCTITAIDTTDVAKNIWKAVFRPHAGNWDIGFHSPCASEGCPDIMFPYFTCHDYKGMMCCFNLTMEVCCKQPRPTGIYMMVERMRIMNNREFAGFKHYREEHIKHYWRFGIFASPFVICWSPKTKGPPTSDWYMRDSEVVTQESELKESWQDMMEQHSMFGIPHCEKERWMNDNWKCKLFYYEVILWISNCECDQHVNCCVAHDPGTQVDWAWTLDMWWDQKYFGFFVRKKGQKYNMHWGAPYWLTNPTEKKDFIQHEQLGPLQTFRHCSSPAPT");
echo $result."\n";
//prints 884608