PHP Demo

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<?php

#require_once "DB.php";

	$host		=	'localhost';
	$user		=	'root';
	$pass		=	'';
	$database	=	'';

$dbc = mysqli_connect($host,$user,$pass,$database);
$sql = "select * from pokemon where National_Pokedex=".$_GET['id'];
#print $sql;
$result = mysqli_query($dbc,$sql);
$row = mysqli_fetch_array($result);
print "<h1>Details of $row[1] <i>($row[0])</i> </h1>";

print "<img src='http://upload.wikimedia.org/wikipedia/en/2/21/001Bulbasaur.png' /><p>";

print "Japenese Name = ".$row[2]."<br>";

$sql2 = "select * from pokemon where National_Pokedex=".$row[3];

#print $sql2;
$result2 = mysqli_query($dbc,$sql2);
$row2 = mysqli_fetch_array($result2);
print "Evolution = ".$row[3]."<br>";
print "Evolution (name) = ".$row2[1]."<br>";

print "<a href='index.php'>Go Back</a>";

#while ($row = mysqli_fetch_array($result)){
#echo "<a href='details.php?id=".$row['National_Pokedex']."'>".$row['English_name']."</a><br>";
#}

?>

Updated version

Bioperl Live

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# script for looping over genbank entries, printing out name

use Bio::DB::Genbank;
use Data::Dumper;

$gb = new Bio::DB::GenBank();
$sequence_object = $gb->get_Seq_by_id('JQ072023');
print Dumper ($sequence_object);
$seq1_id = $sequence_object->display_id();
$seq1_s = $sequence_object->seq();

print "seq1 display id is $seq1_id \n";

print "seq1 sequence is $seq1_s \n";

Bioinformatics II

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Bioinformatica II

Theorieles  9.00-11:30 Lokaal A1.057
Practica  16.00-18u40 PC zaal C

  • do 16 februari: Geen Les
  • do 23 februari: Geen Les
  • do 1 maart: Recap Bioinformatics I, RDBMS, (Bio)SQL
  • do 8 maart: Web Application Developent (PHP)
  • do 15 maart: MyGenBank
  • do 22 maart: Genome Browsers
  • do 29 maart:  Galaxy
  • do 5 april: Geen Les
  • do 12 april: Geen Les
  • do 19 april: Datamining (Tim De Meyer)
  • do 26 april: Textmining (Maté Ongenaert)
  • do 3 mei: Systems Biology (Bart Deplancke)
  • do 10 mei: Les 10  (projectvoorstelling)

CpG counter

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use strict;
use Bio::SeqIO;
use Data::Dumper; 

my $filename="promoter.txt";
my $sequence_object; 

my $seqio = Bio::SeqIO -> new   (
'-format' => 'fasta',
'-file' => $filename);

while ($sequence_object = $seqio -> next_seq) {
#print Dumper($sequence_object);
my $sequentie = $sequence_object-> seq();
print $sequentie."\n";
#last;
my $count=$sequentie=~ s/CG/CG/g;
print "$count\n";
}

Bioperl

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use strict;
use Bio::SeqIO;
use Data::Dumper;

my $filename="swiss-prot.dat";
my $sequence_object;

my $seqio = Bio::SeqIO -> new   (
                                '-format' => 'swiss',
                                '-file' => $filename
                                );

while ($sequence_object = $seqio -> next_seq) {
#print Dumper($sequence_object);
my $sequentie = $sequence_object-> seq();
print $sequentie."\n";
#last;
}