README

BioPHP 实现了一系列用于操作基因组数据的简单工具。它旨在构建基本的RNA、DNA和蛋白质操作工具。BioTorrents.de的分支是为biotorrents/gazelle设计的，并大量受到了TimothyStiles/poly的启发。

简单用法（待修订）

查找反向互补序列

$BioPHP = new BioPHP();
$result = $BioPHP->reverse('ATGAAAGCATC');
$result = $BioPHP->complement($result);
//prints TTTCAT

计算GC含量

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

计算两个序列之间的点突变数量

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

将DNA序列翻译成氨基酸序列

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

计算单同位素质量

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

在DNA中查找基序

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

获取阅读框架

$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()

找到最可能的共同祖先

$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

从Uniprot获取fasta结果并计算同位素质量

$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

使用可变“缩写”基序搜索查找蛋白质基序

$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.

查找共享基序

这项任务可能非常耗费CPU资源。使用PHP 7，这种方法比Python快！运行结果大约为1秒，使用了100个长度为1 kbp的DNA字符串集合。

$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

从DNA序列中找到开放阅读框

$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
)

*/

定位长度为4到12之间的限制性位点

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

从蛋白质推断mRNA - 计算蛋白质可以翻译的所有不同的RNA字符串

注意：此方法需要使用PHP Math Big Integer包，这是此项目的composer依赖项。

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