BioPHP - Sequence Manipulation and Data
Original code submitted by josebaCode bellow is covered by GNU GPL v2 license.
Description
Last change: 2011/04/27 11:01 | Recent Changes | Original descriptionThe sequence is manipulate to remove non-coding characters, to get reverse and complement strands, to obtain both strands, to calculate G+C content and nucleotide composition, or may be converted to RNA.
Code
Last change: 2011/04/27 11:01 | Recent Changes | Download | Original code and
<?php
// author Joseba Bikandi
// license GNU GPL v2
// source code available at biophp.org
// the code in the top will manipulated the input sequence
// in the middle of the file is located the form
// in the botton are located the functions used in this script
//############################################################################
//################# lets manipulated the sequence #################
//############################################################################
if($_POST){
$seq=$_POST["seq"];
$action=$_POST["action"];
// remove non coding (works by default)
$seq=remove_non_coding($seq);
// if subsequence is requested
if ($_POST["start"] or $_POST["end"]){
if($_POST["start"]!=""){$start=$_POST["start"]-1;}else{$start=0;}
if($_POST["end"]!=""){$end=$_POST["end"];}else{$end=strlen($seq);}
$seq=substr($seq,$start,$end-$start);
}
// length of sequence
$seqlen=strlen($seq);
if($action=="reverse"){
// reverse the sequence
$seq=strrev($seq);
}
if($action=="complement"){
// get the complementary sequence
$seq=Complement($seq);
}
if($action=="reverse_and_complement"){
// reverse the sequence
$seq=strrev($seq);
// get the complementary sequence
$seq=Complement($seq);
}
$result="";
if($action=="display_both_strands"){
// get a string with results
$result=Display_both_strands($seq);
}
if($action=="toRNA"){
// get a string with results
$result=toRNA($seq);
}
if($_POST["GC"]==1){
// calculate G+C content
$result.=GC_content($seq);
}
if ($_POST["ACGT"]==1){
// calculate nucleotide conposition
$result.=ACGT_content($seq);
}
// 70 characters per line before output
$seq = chunk_split($seq, 70);
}else{
$seq="";
}
//############################################################################
//################# we have already manipulated the sequence #################
//############################# bellow is the form ###########################
//############################################################################
?>
<html>
<head>
<title>DNA sequence manipulation</title>
</head>
<body bgcolor=FFFFFF>
<center>
<H2>DNA sequence manipulation</H2>
<form method='post' action="<? print $_SERVER["PHP_SELF"]; ?>">
<table cellpadding=5 width=650 border=0 bgcolor=DDFFFF>
<tr><td>
<B>Sequence <?php if($seq){print "($seqlen bp)";} ?>:</B>
</td></tr>
<tr><td>
<textarea name='seq' rows='8' cols='80'><?php print $seq ?></textarea>
</td></tr>
<tr><td>
<select name=action size=7>
<option value=remove_non_coding>Remove no coding characters
<option value=reverse>Reverse sequence
<option value=complement>Complement sequence
<option value=reverse_and_complement>Reverse and Complement of sequence
<option value=display_both_strands>Display Double-stranded Sequence
<option value=toRNA>Convert to RNA
</select>
<br>Select subsequence from position <input type=text name=start size=4> to <input type=text name=end size=4> (both included)
</td></tr>
<tr><td>
<input type=checkbox name=GC value=1> G+C content
<br><input type=checkbox name=ACGT value=1> Nucleotide composition
</td></tr>
<tr><td align=center>
<input type='submit' value='Sutmit'>
</td></tr>
<?php
if($other_results!=""){
print "<tr><td align=center>";
print "<textarea rows=10 cols=80>$other_results</textarea>";
print "</td></tr>";
}
?>
</table>
</form>
<table cellpadding=5 width=650 border=0>
<tr><td>
<pre><?php print $result; ?></pre>
</td></tr>
<tr><td>
<b>NOTES</b>:
<br>Non-coding characters will be removed by default, and X is replaced by N.
<br><a href=http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&list_uids=7957164&dopt=abstract>NC-UIBMB</a>
codes are used as a reference.
<p>Source code is available at
<a href=http://www.biophp.org/minitools/sequence_manipulation_and_data>BioPHP.org</a>
</td></tr>
</table>
</center>
</body>
</html>
<?php
//############################################################################
//################# Functions used in this script ############################
//############################################################################
function Complement($seq){
// change the sequence to upper case
$seq = strtoupper ($seq);
// the system used to get the complementary sequence is simple but fas
$seq=str_replace("A", "t", $seq);
$seq=str_replace("T", "a", $seq);
$seq=str_replace("G", "c", $seq);
$seq=str_replace("C", "g", $seq);
$seq=str_replace("Y", "r", $seq);
$seq=str_replace("R", "y", $seq);
$seq=str_replace("W", "w", $seq);
$seq=str_replace("S", "s", $seq);
$seq=str_replace("K", "m", $seq);
$seq=str_replace("M", "k", $seq);
$seq=str_replace("D", "h", $seq);
$seq=str_replace("V", "b", $seq);
$seq=str_replace("H", "d", $seq);
$seq=str_replace("B", "v", $seq);
// change the sequence to upper case again for output
$seq = strtoupper ($seq);
return $seq;
}
function remove_non_coding($seq) {
// change the sequence to upper case
$seq=strtoupper($seq);
// remove non-words (\W), con coding ([^ATGCYRWSKMDVHBN]) and digits (\d) from sequence
$seq=preg_replace("/\W|[^ATGCYRWSKMDVHBN]|\d/","",$seq);
// replace all X by N (to normalized sequences)
$seq=preg_replace("/X/","N",$seq);
return $seq;
}
function Display_both_strands($seq) {
// get the complementary sequence
$revcomp=Complement($seq);
$result="";
$i=0;
while ($i<strlen($seq)){
if(strlen($seq)<($i+70)){$j=strlen($seq);}else{$j=$i;}
$result.=substr($seq,$i,70)."\t$j\n";
$result.=substr($revcomp,$i,70)."\t$j\n";
$result.="\n"; //line break
$i+=70;
}
return $result;
}
function GC_content($seq) {
$number_of_G=substr_count($seq,"G");
$number_of_C=substr_count($seq,"C");
$gc_porcentaje=round(100*($number_of_G+$number_of_C)/strlen($seq),2);
return "G+C %: $gc_porcentaje\n\n";
}
function toRNA($seq) {
// replace T by U
$seq=preg_replace("/T/","U",$seq);
$seq=chunk_split($seq, 70);
return $seq;
}
function ACGT_content($seq) {
$result="Nucleotide composition";
$result.="\nA: ".substr_count($seq,"A");
$result.="\nC: ".substr_count($seq,"C");
$result.="\nG: ".substr_count($seq,"G");
$result.="\nT: ".substr_count($seq,"T");
if (substr_count($seq,"Y")>0){$result.="\nY: ".substr_count($seq,"Y");}
if (substr_count($seq,"R")>0){$result.="\nR: ".substr_count($seq,"R");}
if (substr_count($seq,"W")>0){$result.="\nW: ".substr_count($seq,"W");}
if (substr_count($seq,"S")>0){$result.="\nS: ".substr_count($seq,"S");}
if (substr_count($seq,"K")>0){$result.="\nK: ".substr_count($seq,"K");}
if (substr_count($seq,"M")>0){$result.="\nM: ".substr_count($seq,"M");}
if (substr_count($seq,"D")>0){$result.="\nD: ".substr_count($seq,"D");}
if (substr_count($seq,"V")>0){$result.="\nV: ".substr_count($seq,"V");}
if (substr_count($seq,"H")>0){$result.="\nH: ".substr_count($seq,"H");}
if (substr_count($seq,"B")>0){$result.="\nB: ".substr_count($seq,"B");}
if (substr_count($seq,"N")>0){$result.="\nN: ".substr_count($seq,"N");}
$result.="\n\n";
return $result;
}
//############################################################################
//############################### End of fuctions ############################
//############################################################################
?>