Bioinformatics.be

Bioinformatics II

admin — Tue, 17 Jan 2012 12:15:04 +0000

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)

And the winners are …

admin — Thu, 08 Dec 2011 15:26:59 +0000

Matthijs Vynck en Bob Van Hove. Congratulations and your names are immortalized on BPC. Special thanks to Joachim De Schrijver for organizing the 2011 edition.

Practicum examen

admin — Thu, 01 Dec 2011 15:20:09 +0000

Genome Gaming

admin — Thu, 24 Nov 2011 17:36:39 +0000

How to play with genetic information. Imagine this on a social network … with your DNA.

Thesisonderwerpen

admin — Thu, 24 Nov 2011 17:26:24 +0000

Volgende week donderdag 1 december zal de les beginnen om 13u15 met een korte voorstelling van de lopende onderzoekslijnen binnen Biobix en de daaraan gekoppelde thesismogelijkheden.

CpG counter

admin — Thu, 24 Nov 2011 15:28:05 +0000

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

admin — Thu, 10 Nov 2011 16:23:09 +0000

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;
}

Genomic Pyramids

admin — Tue, 01 Nov 2011 08:41:06 +0000

The bioinformatics programming challenge 2011 started today 1-11-11 at 11:11am. Answers to be submitted before 30-11-11 at 23:59pm. I love the smell of crunched numbers in the morning.

Bioinformatics Programming Challenge 2011

admin — Sat, 29 Oct 2011 13:14:09 +0000

BPC 2011, the bioinformatics programming challenge is about to be launched 01-11-11. For those of you who need warming up there is an excellent Python Challenge, a game in which each level can be solved by a bit of (Python/Perl) programming.

Prosite scanner

admin — Thu, 27 Oct 2011 14:59:32 +0000

use warnings;
open(FH,"prosite.dat") || die "Problem reading file";
while () {
if (/^ID\s\s\s(.+);/) {$c++;$name=$1}
if (/^PA\s\s\s(.+)\./) {$prosite{$name}=$1;}
#solve multiline patterns ... last;
}
@seq=("MGNLFENCTHRYSFEYIYENCTNTTNQCGLIRNVASSIDVFHWLDVYISTTIFVISGILNFYCLFIALYT YYFLDNETRKHYVFVLSRFLSSILVIISLLVLESTLFSESLSPTFAYYAVAFSIYDFSMDTLFFSYIMIS LITYFGVVHYNFYRRHVSLRSLYIILISMWTFSLAIAIPLGLYEAASNSQGPIKCDLSYCGKVVEWITCS LQGCDSFYNANELLVQSIISSVETLVGSLVFLTDPLINIFFDKNISKMVKLQLTLGKWFIALYRFLFQMT NIFENCSTHYSFEKNLQKCVNASNPCQLLQKMNTAHSLMIWMGFYIPSAMCFLAVLVDTYCLLVTISILK SLKKQSRKQYIFGRANIIGEHNDYVVVRLSAAILIALCIIIIQSTYFIDIPFRDTFAFFAVLFIIYDFSILSLLGSFTGVAM MTYFGVMRPLVYRDKFTLKTIYIIAFAIVLFSVCVAIPFGLFQAADEIDGPIKCDSESCELIVKWLLFCI ACLILMGCTGTLLFVTVSLHWHSYKSKKMGNVSSSAFNHGKSRLTWTTTILVILCCVELIPTGLLAAFGK SESISDDCYDFYNANSLIFPAIVSSLETFLGSITFLLDPIINFSFDKRISKVFSSQVSMFSIFFCGKR","MLDDRARMEA AKKEKVEQIL AEFQLQEEDL KKVMRRMQKE MDRGLRLETH EEASVKMLPT YVRSTPEGSE VGDFLSLDLG GTNFRVMLVK VGEGEEGQWS VKTKHQMYSI PEDAMTGTAE MLFDYISECI SDFLDKHQMK HKKLPLGFTF SFPVRHEDID KGILLNWTKG FKASGAEGNN VVGLLRDAIK RRGDFEMDVV AMVNDTVATM ISCYYEDHQC EVGMIVGTGC NACYMEEMQN VELVEGDEGR MCVNTEWGAF GDSGELDEFL LEYDRLVDES SANPGQQLYE KLIGGKYMGE LVRLVLLRLV DENLLFHGEA SEQLRTRGAF ETRFVSQVES DTGDRKQIYN ILSTLGLRPS TTDCDIVRRA CESVSTRAAH MCSAGLAGVI NRMRESRSED VMRITVGVDG SVYKLHPSFK ERFHASVRRL TPSCEITFIE SEEGSGRGAA LVSAVACKKA CMLGQ","MESDSFEDFLKGEDFSNYSYSSDLPPFLLDAAPCEPESLEINKYFVVIIYVLVFLLSLLGNSLVMLVILY SRVGRSGRDNVIGDHVDYVTDVYLLNLALADLLFALTLPIWAASKVTGWIFGTFLCKVVSLLKEVNFYSGILLLACISVDRY LAIVHATRTLTQKRYLVKFICLSIWGLSLLLALPVLIFRKTIYPPYVSPVCYEDMGNNTANWRMLLRILP QSFGFIVPLLIMLFCYGFTLRTLFKAHMGQKHRAMRVIFAVVLIFLLCWLPYNLVLLADTLMRTWVIQET CERRNDIDRALEATEILGILGRVNLIGEHWDYHSCLNPLIYAFIGQKFRHGLLKILAIHGLISKDSLPKDSRPSFVGSSSGH TSTTL","MEANFQQAVK KLVNDFEYPT ESLREAVKEF DELRQKGLQK NGEVLAMAPA FISTLPTGAE TGDFLALDFG GTNLRVCWIQ LLGDGKYEMK HSKSVLPREC VRNESVKPII DFMSDHVELF IKEHFPSKFG CPEEEYLPMG FTFSYPANQV SITESYLLRW TKGLNIPEAI NKDFAQFLTE GFKARNLPIR IEAVINDTVG TLVTRAYTSK ESDTFMGIIF GTGTNGAYVE QMNQIPKLAG KCTGDHMLIN MEWGATDFSC LHSTRYDLLL DHDTPNAGRQ IFEKRVGGMY LGELFRRALF HLIKVYNFNE GIFPPSITDA WSLETSVLSR MMVERSAENV RNVLSTFKFR FRSDEEALYL WDAAHAIGRR AARMSAVPIA SLYLSTGRAG KKSDVGVDGS LVEHYPHFVD MLREALRELI GDNEKLISIG IAKDGSGIGA ALCALQAVKE KKGLA MEANFQQAVK KLVNDFEYPT ESLREAVKEF DELRQKGLQK NGEVLAMAPA FISTLPTGAE TGDFLALDFG GTNLRVCWIQ LLGDGKYEMK HSKSVLPREC VRNESVKPII DFMSDHVELF IKEHFPSKFG CPEEEYLPMG FTFSYPANQV SITESYLLRW TKGLNIPEAI NKDFAQFLTE GFKARNLPIR IEAVINDTVG TLVTRAYTSK ESDTFMGIIF GTGTNGAYVE QMNQIPKLAG KCTGDHMLIN MEWGATDFSC LHSTRYDLLL DHDTPNAGRQ IFEKRVGGMY LGELFRRALF HLIKVYNFNE GIFPPSITDA WSLETSVLSR MMVERSAENV RNVLSTFKFR FRSDEEALYL WDAAHAIGRR AARMSAVPIA SLYLSTGRAG KKSDVGVDGS LVEHYPHFVD MLREALRELI GDNEKLISIG IAKDGSGIGA ALCALQAVKE KKGLA");
foreach (keys %prosite) {
$name = $_;
$patroon=$prosite{$_};
print "$name\t$patroon\n";
$patroon=~ s/-//g;
$patroon=~ s/x/[ABCDEFGHIKLMNPQRSTVWXYZ]/g;
$patroon=~ s/\(/\{/g;
$patroon=~ s/\)/\}/g;
print "regex: $patroon\n";
foreach $seq(@seq) {
$c++;$seq =~ s/ //g;
#print "\$seq$c:$seq\n";
while ($seq=~ /$patroon/g)
{$p=pos($seq)-length($&)+1;
print "found $name $& in \$seq$c \@$p\n";}
}
#last;
}