Difference between revisions of "Task5 Hemochromatosis Protocol"

From Bioinformatikpedia
(→‎SNPedia)
(→‎HGMD)
Line 17: Line 17:
   
 
We used the non-professional version of [http://www.hgmd.org/ HGMD] and looked for SNPs using the gene symbol HFE as query.
  
We used the non-professional version of [http://www.hgmd.org/ HGMD] and looked for SNPs using the gene symbol HFE as query.
  +
  +
In order to get the SNP statistics the following script was used:
  +
  +
<source lang="perl">
  +
#!/usr/local/bin/perl
  +
use strict;
  +
use warnings;
  +
use diagnostics;
  +
use sigtrap;
  +
use autodie;
  +
  +
my $inFile = "HFE.htm";
  +
my $outFile = "HGMD.txt";
  +
  +
  +
open (IN, "<", $inFile) or die ("Could not open input file!");
  +
open (OUT, ">", $outFile) or die ("Could not open output file!");
  +
  +
#print header
  +
print OUT "ID\tType\tCodon change\tAmino acid change\tPosition\tPhenotype\tReference\n";
  +
  +
while (<IN>)
  +
{
  +
my $line = $_;
  +
my $dummy = $line;
  +
  +
$dummy=~s/\s//gi;
  +
  +
if ($dummy ne "")
  +
{
  +
my @content = split(/<\/td>/, $line);
  +
  +
my $id = $content[0];
  +
my $type;
  +
my $codon = $content[1];
  +
my $aa = $content[2];
  +
my $pos = $content[3];
  +
my $phenotype = $content[5];
  +
my $ref = $content[6];
  +
my $link;
  +
  +
$id =~m/>(\w+?)</gi;
  +
$id = $1;
  +
  +
$codon =~m/>([\w-]+?)$/gi;
  +
$codon = $1;
  +
  +
$aa =~m/>([\w-]+?)$/gi;
  +
$aa = $1;
  +
  +
$pos =~m/>(\d+?)$/gi;
  +
$pos = $1;
  +
  +
$phenotype =~m/>([\w\s,?]+?)$/gi;
  +
$phenotype = $1;
  +
  +
$ref =~m/^<.*?href="(.+?)">(.*?)<\/a>/gi;
  +
$link = $1;
  +
$ref = $2;
  +
$ref =~ s/<.*?>//gi;
  +
  +
if ($aa =~m/Term/gi)
  +
{
  +
$type = "Nonsense";
  +
}
  +
elsif ($aa =~m/^(.+?)-(.+?)$/g && $1 eq $2)
  +
{
  +
$type = "Synonymous";
  +
}
  +
else
  +
{
  +
$type = "Non-synonymous";
  +
}
  +
  +
print OUT "$id\t$type\t$codon\t$aa\t$pos\t$phenotype\t[$link $ref]\n";
  +
}
  +
}
  +
  +
close IN;
  +
close OUT;
  +
</source>
   
 
<br style="clear:both;">
  
<br style="clear:both;">

Revision as of 14:04, 10 June 2012

Translation and alignment tools

  • Translation (RNA/DNA->AA): Link
  • Online alignment: Link
  • Reference protein sequence: Q30201


SNP search


HGMD

We used the non-professional version of HGMD and looked for SNPs using the gene symbol HFE as query.

In order to get the SNP statistics the following script was used:

<source lang="perl">

  1. !/usr/local/bin/perl

use strict; use warnings; use diagnostics; use sigtrap; use autodie;

my $inFile = "HFE.htm"; my $outFile = "HGMD.txt";


open (IN, "<", $inFile) or die ("Could not open input file!"); open (OUT, ">", $outFile) or die ("Could not open output file!");

  1. print header

print OUT "ID\tType\tCodon change\tAmino acid change\tPosition\tPhenotype\tReference\n";

while (<IN>) { my $line = $_; my $dummy = $line;

$dummy=~s/\s//gi;

if ($dummy ne "") { my @content = split(/<\/td>/, $line);

my $id = $content[0]; my $type; my $codon = $content[1]; my $aa = $content[2]; my $pos = $content[3]; my $phenotype = $content[5]; my $ref = $content[6]; my $link;

$id =~m/>(\w+?)</gi; $id = $1;

$codon =~m/>([\w-]+?)$/gi; $codon = $1;

$aa =~m/>([\w-]+?)$/gi; $aa = $1;

$pos =~m/>(\d+?)$/gi; $pos = $1;

$phenotype =~m/>([\w\s,?]+?)$/gi; $phenotype = $1;

$ref =~m/^<.*?href="(.+?)">(.*?)<\/a>/gi; $link = $1; $ref = $2; $ref =~ s/<.*?>//gi;

if ($aa =~m/Term/gi) { $type = "Nonsense"; } elsif ($aa =~m/^(.+?)-(.+?)$/g && $1 eq $2) { $type = "Synonymous"; } else { $type = "Non-synonymous"; }

print OUT "$id\t$type\t$codon\t$aa\t$pos\t$phenotype\t[$link $ref]\n"; } }

close IN; close OUT; </source>


dbSNP


SNPdbe

We've searched SNPdbe for SNPs using NP_000401, Q30201, and HFE as query IDs.


OMIM

We searched OMIM for the HFE Gene and looked at the listed allelic variants.


SNPedia

For SNPedia we looked at the SNPs listed under HFE.


Mapping


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