Difference between revisions of "Journal Task4 PKU"

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(Created page with "Phenylketonuria » Homology based structure predictions » Journal <hr>")
 
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[[Phenylketonuria]] » [[Homology-based_structure_prediction_(PKU)|Homology based structure predictions]] » Journal
 
[[Phenylketonuria]] » [[Homology-based_structure_prediction_(PKU)|Homology based structure predictions]] » Journal
 
<hr>
 
<hr>
  +
== Datasets ==
  +
To get homologous structures we performed three different searches with three different web-services and compared them to our findings from [[Sequence_Search_and_Multiple_Sequence_Alignment_(PKU)#Datasets|Task2]].
  +
We got three outputfiles which were parsed and the related files got downloaded from the PDB by using these scripts
  +
===HHPred===
  +
<source lang="perl">
  +
my $id;
  +
my $Evalue;
  +
my $Identities;
  +
my $bool = "F";
  +
  +
open(IN,"<". $ARGV[0]);
  +
open(OUT80, ">dataset_80.txt");
  +
open(OUT40, ">dataset_40.txt");
  +
open(OUT20, ">dataset_20.txt");
  +
  +
mkdir("output");
  +
  +
while(<IN>) {
  +
chomp;
  +
if( ($_ =~ /^>\d+/ )) {
  +
$_ =~ />(.{4}).+/;
  +
$id = $1;
  +
$bool ="T";
  +
}
  +
if($bool eq "T" && $_ =~ /^.*Probab/)
  +
{
  +
$_ =~ /^.*Probab=.+E-value=(.+)\s+Score=.+Aligned_cols=.+Identities=(.+)%\s+Similarity=.+/;
  +
$bool ="F";
  +
$Evalue = $1;
  +
$Identities = $2;
  +
if($Evalue <= $ARGV[1] && $Identities > 80){
  +
print OUT80 "$id\t$Evalue\t$Identities\n";
  +
@args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=output/$id.pdb");
  +
system(@args) == 0 or die "system @args failed: $?"
  +
}
  +
elsif($Evalue <= $ARGV[1] && $Identities < 30){
  +
print OUT20 "$id\t$Evalue\t$Identities\n";
  +
@args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=output/$id.pdb");
  +
system(@args) == 0 or die "system @args failed: $?"
  +
}
  +
elsif($Evalue <= $ARGV[1] && $Identities > 40)
  +
{
  +
print OUT40 "$id\t$Evalue\t$Identities\n";
  +
@args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=output/$id.pdb");
  +
system(@args) == 0 or die "system @args failed: $?"
  +
}
  +
}
  +
}
  +
close OUT80;
  +
close OUT40;
  +
close OUT20;
  +
</source>
  +
  +
=== Coma ===
  +
<source lang="perl">
  +
my $id;
  +
my $Evalue;
  +
my $Identities;
  +
my $Positives;
  +
my $bool = "F";
  +
  +
open(IN,"<". $ARGV[0]);
  +
open(OUT80, ">dataset_coma_80.txt");
  +
open(OUT40, ">dataset_coma_40.txt");
  +
open(OUT20, ">dataset_coma_20.txt");
  +
  +
mkdir("outputcoma");
  +
  +
while(<IN>) {
  +
chomp;
  +
if( ($_ =~ /^>\d+/ )) {
  +
$_ =~ />(.{4}).+/;
  +
$id = $1;
  +
$bool ="T";
  +
}
  +
elsif($bool eq "T" && $_ =~ /^Score/){
  +
$_ =~ /.+Expect\s+=\s+(.+)\s+P-value.+/;
  +
$Evalue = $1;
  +
}
  +
elsif($bool eq "T" && $_ =~ /^Identities/)
  +
{
  +
$_ =~ /Identities.+\((\d+)%\)\s+Positives.+\((\d+)%\)\s+Gaps.+/;
  +
$bool ="F";
  +
$Identities = $1;
  +
$Positives = $2;
  +
if($Evalue <= $ARGV[1] && $Identities > 80){
  +
print OUT80 "$id\t$Evalue\t$Identities\t$Positives\n";
  +
@args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=outputcoma/$id.pdb");
  +
system(@args) == 0 or die "system @args failed: $?"
  +
}
  +
elsif($Evalue <= $ARGV[1] && $Identities < 30){
  +
print OUT20 "$id\t$Evalue\t$Identities\t$Positives\n";
  +
@args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=outputcoma/$id.pdb");
  +
system(@args) == 0 or die "system @args failed: $?"
  +
}
  +
elsif($Evalue <= $ARGV[1] && $Identities > 40)
  +
{
  +
print OUT40 "$id\t$Evalue\t$Identities\t$Positives\n";
  +
@args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=outputcoma/$id.pdb");
  +
system(@args) == 0 or die "system @args failed: $?"
  +
}
  +
}
  +
}
  +
  +
close OUT80;
  +
close OUT40;
  +
close OUT20;
  +
</source>

Revision as of 16:06, 30 May 2012

Phenylketonuria » Homology based structure predictions » Journal


Datasets

To get homologous structures we performed three different searches with three different web-services and compared them to our findings from Task2. We got three outputfiles which were parsed and the related files got downloaded from the PDB by using these scripts

HHPred

<source lang="perl"> my $id; my $Evalue; my $Identities; my $bool = "F";

open(IN,"<". $ARGV[0]); open(OUT80, ">dataset_80.txt"); open(OUT40, ">dataset_40.txt"); open(OUT20, ">dataset_20.txt");

mkdir("output");

while(<IN>) { chomp; if( ($_ =~ /^>\d+/ )) { $_ =~ />(.{4}).+/; $id = $1; $bool ="T"; } if($bool eq "T" && $_ =~ /^.*Probab/) { $_ =~ /^.*Probab=.+E-value=(.+)\s+Score=.+Aligned_cols=.+Identities=(.+)%\s+Similarity=.+/; $bool ="F"; $Evalue = $1; $Identities = $2; if($Evalue <= $ARGV[1] && $Identities > 80){ print OUT80 "$id\t$Evalue\t$Identities\n"; @args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=output/$id.pdb"); system(@args) == 0 or die "system @args failed: $?" } elsif($Evalue <= $ARGV[1] && $Identities < 30){ print OUT20 "$id\t$Evalue\t$Identities\n"; @args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=output/$id.pdb"); system(@args) == 0 or die "system @args failed: $?" } elsif($Evalue <= $ARGV[1] && $Identities > 40) { print OUT40 "$id\t$Evalue\t$Identities\n"; @args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=output/$id.pdb"); system(@args) == 0 or die "system @args failed: $?" } } } close OUT80; close OUT40; close OUT20; </source>

Coma

<source lang="perl"> my $id; my $Evalue; my $Identities; my $Positives; my $bool = "F";

open(IN,"<". $ARGV[0]); open(OUT80, ">dataset_coma_80.txt"); open(OUT40, ">dataset_coma_40.txt"); open(OUT20, ">dataset_coma_20.txt");

mkdir("outputcoma");

while(<IN>) { chomp; if( ($_ =~ /^>\d+/ )) { $_ =~ />(.{4}).+/; $id = $1; $bool ="T"; } elsif($bool eq "T" && $_ =~ /^Score/){ $_ =~ /.+Expect\s+=\s+(.+)\s+P-value.+/; $Evalue = $1; } elsif($bool eq "T" && $_ =~ /^Identities/) { $_ =~ /Identities.+\((\d+)%\)\s+Positives.+\((\d+)%\)\s+Gaps.+/; $bool ="F"; $Identities = $1; $Positives = $2; if($Evalue <= $ARGV[1] && $Identities > 80){ print OUT80 "$id\t$Evalue\t$Identities\t$Positives\n"; @args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=outputcoma/$id.pdb"); system(@args) == 0 or die "system @args failed: $?" } elsif($Evalue <= $ARGV[1] && $Identities < 30){ print OUT20 "$id\t$Evalue\t$Identities\t$Positives\n"; @args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=outputcoma/$id.pdb"); system(@args) == 0 or die "system @args failed: $?" } elsif($Evalue <= $ARGV[1] && $Identities > 40) { print OUT40 "$id\t$Evalue\t$Identities\t$Positives\n"; @args = ("wget", "http://pdb.rcsb.org/pdb/files/". $id . ".pdb", "--output-document=outputcoma/$id.pdb"); system(@args) == 0 or die "system @args failed: $?" } } }

close OUT80; close OUT40; close OUT20; </source>