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Genome

The Ultimate Source Code....

Contents 1 Introduction 1.1 DNA 1.1.1 Overview 1.1.2 Keeping up with the Human Genome 2 The Target: Hemoglobin 2.1 Chromosomal Locus 3 Download the Human Genome Code 3.1 Repository 3.2 Genome Reference Consortium Human (GRCh) Build 37 3.2.1 Chromosome 11 3.2.2 Chromosome 16 4 Look at the Language Reference 5 Install the Debugger / Editor 5.1 ugene 6 See the 3D Structure 6.1 Sequence 7 Grep on it 8 Track a Bug 9 Decode

Introduction

DNA

• Packing, Replication and Transcription
• http://www.youtube.com/watch?v=4PKjF7OumYo&NR=1
• Body Code (From Walter+Eliza Hall Medical Foundation)
  • http://www.wehi.edu.au/education/wehi-tv/

Overview

• http://www.metacafe.com/watch/319359/human_genome/
• http://www.youtube.com/watch?v=XuUpnAz5y1g

Keeping up with the Human Genome

• • http://video.google.com/videoplay?docid=-3068967863312207867#

The Target: Hemoglobin

• http://en.wikipedia.org/wiki/Hemoglobin

• Animation of Oxy-Deoxy state
  • http://upload.wikimedia.org/wikipedia/commons/0/07/Hb-animation2.gif

• Animation of Molecular configuration
  • http://upload.wikimedia.org/wikipedia/commons/b/ba/Hemoglobin_t-r_state_ani.gif

• Code Reuse
  • http://upload.wikimedia.org/wikipedia/commons/thumb/4/48/Nur04505.jpg/180px-Nur04505.jpg
  • http://en.wikipedia.org/wiki/Riftia_pachyptila

• Source Code

Subunit	Gene	Chromosomal Locus
Hb α1	HBA1	Chromosome 16 p13.3
Hb α2	HBA2	Chromosome 16 p13.3
Hb β	HBB	Chromosome 11 p15.5

Chromosomal Locus

• http://en.wikipedia.org/wiki/Locus_(genetics)

• http://en.wikipedia.org/wiki/File:Chromarms.gif

p13.3 means

• in the "p" arm (the short arm)
• band 13
• sub-band 3

Download the Human Genome Code

Repository

• http://vimeo.com/1865535
• ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/
• ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/

Genome Reference Consortium Human (GRCh) Build 37

Chromosome 11

 wget ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/hs_ref_GRCh37_chr11.agp.gz
 wget ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/hs_ref_GRCh37_chr11.fa.gz
 wget ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/hs_ref_GRCh37_chr11.mfa.gz

Chromosome 16

 wget ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/hs_ref_GRCh37_chr16.agp.gz
 wget ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/hs_ref_GRCh37_chr16.fa.gz
 wget ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/Assembled_chromosomes/hs_ref_GRCh37_chr16.mfa.gz

Look at the Language Reference

• http://en.wikipedia.org/wiki/Genetic_code

Install the Debugger / Editor

ugene

In Linux

   sudo apt-get install ugene

Or download binaries for Mac and Windows from

      http://ugene.unipro.ru/

See the 3D Structure

http://www.ncbi.nlm.nih.gov/sites/entrez?db=structure&term=HBA1&submit=Go

Sequence

• Open the files GRCCh37 in ugene
• Do CTRL-G and go to location: 226679 to the start of the Gene
• Enable the display of the Aminoacid Translation
• Do CTRL-G and go to location: 226716 to the start of the mRNA translated zone
  • Compare with the genetic code below (Protein Sequence of Aminoacids)

  MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA
  VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK
  YR

GRC Ch37

• http://www.ncbi.nlm.nih.gov/nuccore/NC_000016.9?from=226637&to=227562&report=graph
• http://www.ncbi.nlm.nih.gov/nuccore/224589807?report=fasta

HuRef

• Homo sapiens chromosome 16, alternate assembly HuRef, whole genome shotgun sequence
• http://www.ncbi.nlm.nih.gov/nuccore/AC_000148.1?&from=144721&to=145562&report=graph&strand=true

Protein Sequence of Aminoacids for Hemoglobin HBA1

• http://www.ncbi.nlm.nih.gov/protein/NP_000549.1?report=fasta

Grep on it

Track a Bug

Sickle Cell Dissease

• http://en.wikipedia.org/wiki/Sickle-cell_disease
• The genetic disorder is due to the mutation of a single nucleotide, from a GAG to GTG codon mutation
• The allele responsible for sickle-cell anaemia is autosomal incomplete dominant and can be found on the short arm of chromosome 11
• http://www.nhlbi.nih.gov/health/dci/Diseases/Sca/SCA_WhatIs.html

Decode