Task5 Hemochromatosis Protocol

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>

SNPdbe

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

• Quick-Link: NP_000401
• Quick-Link: Q30201
• Quick-Link: HFE

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.